This article makes a case against burning heretics based, in part, on the words, actions, and general demeanor of Jesus Christ as recorded in the Gospels:
It seems bizarre to me that there are radical Christians who think heretics should be burned at the stake when Jesus emphasized mercy and love for his enemies. He released the woman caught in adultery (John 8:1-11), implored Peter to drop his sword (Matthew 26:52), and most prominently, said, “You have heard that it was said, ‘Love your neighbor and hate your enemy,’ But I tell you, love your enemies and pray for those who persecute you…” (Matthew 5:43-44). It seems an unthinkable response for the radical to say that they are loving someone, by burning them alive. Further, Jesus specifically altered a command for violent punishment in the Law. He said, “You have heard that it was said, ‘Eye for eye, and tooth for tooth.’ But I tell you, do not resist an evil person.” (Matthew 5:38-39). Should heretics be burned at the stake? It seems that the aura and the spirit of these commands combats this radical inclination.
The author goes on to imagine what a world would look like in which heretics were ferreted out of society, captured, and put to death:
If Christians did begin to establish a system in which heretics were burned at the stake, the question is what the world would look like. What would the church look like? If a heretic is being burned at the stake, certainly, his work would also be disposed of (for the same reason that the man is burned alive). So then, what is heresy? How do we identify it, and if someone is practicing heresy, how do we determine who it is? We would have to establish an investigative unit that is finely tuned to hunt out the heretics and their work. They would be licensed to venture into the property of the alleged heretic and conduct a thorough investigation of their writing to ensure that there was nothing heretic lingering about. If it was found, the heretic would be subsequently arrested. They would be told to repent or die. The reader might realize that this would not be the first time that a religious organization has conceived of limiting the freedom of speech through violence. Just thinking of what the world would look like, given that limitation, we are stricken instantly with the acknowledgement that this would look a lot like ISIS and the Inquisition. Of course, these are non-sustainable models of society. Should heretics be burned at the stake? Of course not. That is social regression. That is barbarism.
Balthasar Hubmaier (l. 1480-1528) was a Catholic theologian who converted to the Protestant Anabaptist sect in 1525. His "Concerning Heretics and Those Who Burn Them" (1524) was a plea for religious tolerance written prior to his conversion to a sect persecuted by both Catholics and Protestants who dismissed the piece as heretical.
Here are some interesting bits from an article in worldhistory.org written about Hubmaier's work in which he argues against the practice of killing heretics by every denomination of the Church. The full text of his short work is at the end of the article linked above:
Although Hubmaier wrote the work as a Catholic, it was adopted by the Anabaptists to denounce the practice of both Catholic and Protestant tribunals of charging the unorthodox with heresy and sentencing them to death. The Church had been executing 'heretics' for centuries by this time and, once the Protestant sects established themselves, they retained this practice. Although Catholics and Protestants could not seem to agree on anything else, they found common ground in persecuting the 'other', and their common enemy after 1525 became the Anabaptist sect, which rejected the tenets of both and, except for some radical leaders, advocated pacifism.
Once again the central point of condemnation for the burning of heretics is the contradiction of Jesus' words and model of behavior. He goes farther, however, and labels such activity within and by the church as the work of Satan:
Once Hubmaier became an Anabaptist, his work – like that of all Anabaptists – was condemned as heretical even though he regularly cites the Bible throughout in support of his claims. His central argument is simply that the practice of burning people alive as heretics is unbiblical as it contradicts the words and example of Jesus Christ and so is actually evil and the work of Satan. Hubmaier's piece was widely circulated after publication as he had been a popular Catholic preacher, but after his conversion, he fell out of favor except among Anabaptists. Hubmaier and his wife, Elizabeth (née Hügline) would eventually be executed for heresy in 1528, but his works were preserved by the Anabaptists, who continue to flourish under various names in the present day.
It appears as though the best case to be made from the New Testament against the church sentencing heretics to death is the Lord Jesus Christ himself; both His words and His example. He was condemned to death through religious/political zeal by the dominant "church" of the day and the sentence was carried out by the dominant government of the day. There is not one iota of commendation in the New Testament for either of the parties responsible for Jesus' death.
Every human element, motive, and activity involved in putting the Christ to death is labeled as evil. Evil men, evil motives, and evil activity. That God is able to turn that which is intended for evil unto good commends not us but God. Nowhere does this same Christ recommend putting our religious enemies to death (indeed the opposite is true). Since the Spirit of God cannot be at odds with the Son of God it is impossible for the burning of heretics to be anything other than against the will of the Spirit since it is against the Son.
To condemn and put a person to death as a heretic simply and only because they are labeled as heretics is evil, ungodly activity and against the command and example of the Lord of all. To favor such activity or to ascribe God's commendation to it is equally evil and is, itself, heretical; opposing both God and His Gospel. Killing people who don't believe the same as us is not Christian behavior nor is condemning to death a religious duty.
So that my final paragraphs do not appear as a solitary opinion, here are some of Hubmaier's words on the subject in summary and closing:
Hence it follows that the inquisitors are the greatest heretics of all, since, against the doctrine and example of Christ, they condemn heretics to fire, and before the time of harvest root up the wheat with the tares. For Christ did not come to butcher, destroy, and burn, but that those that live might live more abundantly. If these only knew of what spirit they ought to be, they would not so shamelessly pervert God’s Word, nor so often cry, “To the fire, to the fire!” The secular power rightly and properly puts to death the criminals who injure the bodies of the defenseless (Rom. 13:3,4). But he who is God’s cannot injure anyone, unless he first deserts the gospel.
Hence to burn heretics is in appearance to profess Christ (Titus 1:10,11), but in reality to deny him, and to be more monstrous than Jehoiakim, the King of Judah (Jer. 36:23). Now it is clear to everyone, even the blind, that a law to burn heretics is an invention of the devil. “Truth is immortal.”