More intolerance: the early Church Councils, Crusades, Inquisition and Reformation

"Unbelievers deserve not only to be separated from the Church, but also... to be exterminated from the World by death."
- Saint Thomas Aquinas, Summa Theologica, 1271

The Early Church Councils: murder, heresy and shaping future beliefs

In 380, the Roman Christian Emperor Theodosius passed a decree that read:

"We shall believe in the single Deity of the Father, the Son, and the Holy Spirit, under the concept of equal majesty and of the Holy Trinity. We command that those persons who follow this rule shall embrace the name of Catholic Christians. The rest, however, whom We adjudge demented and insane, shall sustain the infamy of heretical dogmas, their meeting places shall not receive the name of churches, and they shall be smitten first by divine vengeance and secondly by the retribution of Our own initiative, which We shall assume in accordance with the divine judgment."

-- Helen Ellerbe, The Dark Side of Christian History

Already in 385 C.E. the first Christians, the Spanish Priscillianus and six followers, were beheaded for heresy in Trier/Germany
Manichaean heresy: a crypto-Christian sect decent enough to practice birth control (and thus not as irresponsible as faithful Catholics) was exterminated in huge campaigns all over the Roman empire between 372 C.E. and 444 C.E. Numerous thousands of victims.
-- Opus Diaboli, by Karlheinz Deschner

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Repression began as soon as the Christians gained control of the Roman Empire. Constantine jailed and suppressed Christian bishops who supported Arius. Arius was considered a heretic (325 c.e.) who denied the divinity of Jesus Christ, and the unity of the godhead (trinity.) In 385 c.e. The dissident (i.e. heretic) Priscillian and his followers were executed for heresy.

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Roman Christianity persecuting other Christianities:

In 317 Constantine's Roman Christian sectarians in Carthage filled the well outside the main Donatist [non-Roman Christian] church with the bodies of their Christian opponents.

In 333 AD Constantine issued edicts against "Arius, wicked and impious," forbidding his teaching and even outlawing owning the Arian version of the New Testament.

In 382, in Egypt, celebrating Easter on the day set aside by the local non-Roman Christian sect was punishable by death.

In 383, in Spain, Urbanica was stoned to death and her bishop Priscillian was executed for their non-Roman Christian beliefs.

St. Augustine describes the sectarian struggles in North Africa, in which believers had their eyes torn out and one bishop had his hands and tongue cut off. [Augustine, Epistles 44.7]

From: Triumph over other Christianities

Besides determining which books belonged in the Christian Canon, the councils also determined which concepts and beliefs were to become part of Christian doctrine, and which would be classed as heresy and its adherents persecuted. They also decided Church practices, such as moving the Sabbath from Saturday to Sunday.

The history of these councils is both bewildering and abominable. ...Contrary to the naive opinion that the deliberations of church councils were infused by the power of divine guidance, most of the councils — and their aftermaths — were pretty ghastly affairs. [Link]

The Council of Nicaea (A.D. 325): The first Christian Emperor of Rome, Constantine the Great, after having many of his close relatives put to death, convened this Council to determine which of the Christian factions with opposing ideas on the matter of the nature of Jesus should be considered orthodoxy:

The burning question of the council was the argument between Arius and Bishop Alexander of Alexandria. Arius claimed Jesus was essentially distinct from the Father, having been created ex nihilo by the latter. Alexander, however, claimed

"as God is eternal, so is his Son — when the Father, then the Son — the Son is present in God without birth, ever-begotten, an unbegotten-begotten."

By a packed vote, Arius was condemned as a heretic, excommunicated, and exiled. Three years later, however, Constantine ... recalled Arius to Constantinople. On the very day Arius was to reenter the Cathedral in triumph, his bowels suddenly burst out in a privy, obviating any need to redefine orthodoxy. The orthodox considered it a miracle; the Arians knew it was murder.

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Basically, Bishop Alexander of Alexandria claimed that Jesus and his Father were one and the same, whilst Arius and his followers held the doctrine that Jesus was not co-substantial with God - that is, they claimed Jesus was distinct from his Father, God.

In time, the rival doctrines of Arius were declared a heresy. For this, Arianism was persecuted out of existence: since the Northern tribes and many others belonged to this Christian sect, the mainstream Church persecuted the highly numerous Arians to their deaths.
Whenever a vestige of this early heretical Christian sect resurfaced, it would be instantly suppressed. 16th century Protestant England, for instance, burnt an Arian to death.
See also: The Arian Controversy and its demise, how the heretical Arianism was murdered out by Catholicism, more on Arius during Constantine's reign and afterwards

"Ecumenical" Council of Ephesus (A.D. 431): St. Cyril, the Pope of Alexandria, bribed enough bishops to be able to convene the Council before the arrival of the Patriarch of Antioch, whose opposition he feared. Without opposition from the delegation from Antioch it was a simple matter to condemn one Nestorius as a heretic, and to proclaim the Virgin Mary to be theotokos, or "mother of god."

Second Synod of Ephesus (A.D. 449): Dioscoros, the Pope of Alexandria (Cyril's successor), condemned Flavian, the Pope of Constantinople, and then kicked his rival in Christ so severely that he died three days later. Summoning a mob of monks and soldiers wielding staves, swords, and chains, Dioscoros convinced the bishops who had planned to vote for Flavian to vote "correctly."

Such were the means by which truth was determined in the orthodox Catholic Church.

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Nestorian heresy: a closer look

Ecumenical Council of Ephesus (431): denounced the teachings of Nestorius (d. 451), who argued that Christ had completely separate human and divine natures.

Link has more: the Three Chapters dispute, Monophysitism troubles and dealing with Monotheletism.
Like Arianism and Priscillian's followers, the Nestorian sects would in time be persecuted as heretics too.

The History of the Conflict Between Religion and Science by John William Draper briefly recounts the argument about Mary between Nestor(ius), the Bishop of Antioch, and Bishop Cyril of Alexandria:

Cyril was determined that the worship of the Virgin as the Mother of God should be recognized, Nestor was determined that it should not. In a sermon delivered in the metropolitan church at Constantinople, he vindicated the attributes of the Eternal, the Almighty God. "And can this God have a mother?" he exclaimed. In other sermons and writings, he set forth with more precision his ideas that the Virgin should be considered not as the Mother of God, but as the mother of the human portion of Christ, that portion being as essentially distinct from the divine...

For this, Nestor and his followers were persecuted and fled:

The overthrow and punishment of Nestor, however, by no means destroyed his opinions. He and his followers, insisting on the plain inference of the last verse of the first chapter of St. Matthew, together with the fifty-fifth and fifty-sixth verses of the thirteenth of the same gospel, could never be brought to an acknowledgment of the perpetual virginity of the new queen of heaven. ...While their leader was tormented in an African oasis, many of them emigrated to the Euphrates, and established the Chaldean Church. Under their auspices the college of Edessa was founded. From the college of Nisibis issued those doctors who spread Nestor's tenets through Syria, Arabia, India, Tartary, China, Egypt.

Among a countless host of disputants may be mentioned Arians, Basilidians, Carpocratians, Collyridians, Eutychians, Gnostics, Jacobites, Marcionites, Marionites, Nestorians, Sabellians, Valentinians.
Of these, the Marionites regarded the Trinity as consisting of God the Father, God the Son, and God the Virgin Mary; the Collyridians worshiped the Virgin as a divinity, offering her sacrifices of cakes; the Nestorians, as we have seen, denied that God had "a mother."
...But, though they were irreconcilable in matters of faith, there was one point in which all these sects agreed - ferocious hatred and persecution of each other.

Those whose turn it was to be persecuted, would flee to pluralistic, non-Christian, pre-Islamic Arabia which had since ages given home to refugees. Unfortunately, as increasing numbers of heretical Christian communities found refuge there, Churches started dotting the Arabian countryside too. Christians frantically went about making converts from among the various unwilling pagan Arabian clans. The Nestorians of Abyssinia then took over pagan Yemen in Southern Arabia, to rule over and convert.
From Nestorianism to Monothelitism shows that Nestorius wasn't tolerant either and condemned others' ideas as heretical in his turn. In this he was no different from other early Christian sects:

Africa was equally disturbed by the factions of the rival bishops Caecilian and Donatus, which afflicted its provinces above three hundred years, the feud being only extinguished when Christianity was overcome by Mohammedanism. Excommunicated by the Western Church, the Donatists boldly excommunicated all other churches than their own.
-- Crimes of Christianity, by G W Foote and J M Wheeler

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The Church fathers

...
It will be said that the Fathers were as good as their times. That can not be maintained. They were not even as good. There were men in those days who saw that the world was round. The fact that Augustine, Lactantius, and other Fathers, opposed the theory, shows that there were men who advocated it. ... Yet the writers could not see that the arguments were valid, whereas other men could. In short, the sum of the charge against the Fathers is that they were not competent to tell what was evidence of a fact and what was not.

But one apology has ever been made for these remarkable errors of the Fathers, and that is "spiritual insight." Christian defenders say that, while the Fathers were ignorant, and even superstitious, they were yet "gifted with great spiritual insight." This term signifies the possibility of perceiving something which does not exist and where it does not exist. It is synonymous with "unlimited credulity."

Not alone in nature, but also in literature, the Fathers were ignorant and unscholarly. Jerome and Origen were the only ones who could read Hebrew,1 unless we except Dorotheus.2 Justin Martyr quotes from Jeremiah and calls it Isaiah.3 Clement of Alexandria quotes as Scripture passages which are not in the Bible.4 He quotes as Paul's, words which are not in Paul.5 In quoting from an opponent he would insert—not with intent to misrepresent, perhaps, but with the same result—words not in the original,6 and he even does the same in quoting from the Bible.7 Tertullian quotes as in Leviticus a passage not in that book;8 he misquotes history;9 he cites as in Isaiah a passage not in that book, but in Revelation,10 and he is frequently inaccurate in quotations. The Gospel writers committed the same blunders. The man who wrote the Gospel of Matthew attributes to Jeremiah11 a passage which is in Zechariah;12 and the writer of the Gospel of Mark attributes to Isaiah13 a passage which is in Malachi.14
-- A Short History of the Bible, by Bronson C. Keeler

Some famous heretical Church fathers
The few among the early Christian Church who were (comparably) able - Tertullian, Origen, and Clement of Alexandria - all became tainted with heresy:

Tertullian, a somber fanatic with a mighty power of scorn, a learned priest of the African Church, remained a heretic until he died. Origen was deposed, excommunicated, and bitterly persecuted... Clement was more diplomatic, and remained within the Church. His writings, however, had a narrow circulation amongst the educated converts of Alexandria.
-- The Story Of Religious Controversy, by Joseph McCabe

See more:

• A timeline of Christian Councils
• The Real Bible - who's got it?
• The Arian Controversy
• Orthodoxy and the Early Church
• From Nestorianism to Monothelitism. About various Church teachings and heresies determined during the Church councils: Apollinarianism and Nestorianism, Euthychianism (Monophysitism) and Monothelitism.
• Christ to Constantine from Crimes of Christianity, by G W Foote and J M Wheeler.
  See also the section St Constantine and the page on Constantine for more about the character of the first Christian Emperor.
• Of the early Church Fathers, some were sainted and others excommunicated, yet even these excommunicated early Christians still tend to be well-respected by members of several denominations. See The Church fathers and Christian Hall of Shame for some of their statements.
  The writings of the heretical Church fathers are even held up as proof of various preposterous positions. For instance, the heretic Tertullian is accredited with having proposed the Trinitarian doctrine. The late Church reasoning about this is that, although the persons themselves might have been heretical, those doctrinal pronouncements of theirs that were accepted by the Church (sometimes through voting) were inspired. 'Inspiration' frequently meant a majority vote was accompanied by threatening and murdering the opposition.
  The early Church fathers were also known for practising and promoting Lying for God - the Christian Way.