Today, heresy is hardly an operative term in Protestant church life, but in Calvin's day to deny the Trinity was tantamount to committing treason against the basic foundation of society itself. Servetus was a hunted man all over Europe. He had been burned in effigy by the Catholics before he was burned in reality by the Protestants, and it could just as easily have been the other way around. Calvin believed that the civil magistrate was the custodian of both tables of the law and should punish heresy, blasphemy, and idolatry no less than murder, theft, and perjury. Roger Williams, a 17th-century Calvinist who preached and practiced religious liberty in early Rhode Island, denied the state any role in compelling obedience to the first table of the law, securing a firmer basis for freedom of conscience.
Calvin worked with a more medieval understanding of the unitary nature of society and thus limited the degree of liberty he was willing to concede to religious dissenters. We can note that the Genevan officials who condemned Servetus to death were actually Calvin's opponents, not his henchmen. We can also point out that religious persecution was commonplace in Calvin's century: Mary Tudor sent hundreds of Protestants to their deaths in England, thousands of Huguenots were killed in the massacre of St. Bartholomew's Day, and many more Dutch Calvinists were slain by the Duke of Alva.
All this is true, but the fact remains that Calvin should have known better. The logic of his own thinking could and should have led him to agree with Sebastian Castellio, his sometime friend and later critic, who declared: "To kill a man is not to defend a doctrine; it is to kill a man."
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