The stake, incarceration, and the triremes are those dramatic forms of penal procedure which are generally associated with inquisitorial practice. But a survey of the thousands of surviving sentences suggests that in actual fact milder forms of punishment prevailed. Most frequently encountered are public humiliation in the form of abjurations read on the cathedral steps on Sundays and feast days before the throngs of churchgoers, and salutary penances, fines or service for the benefit of charitable establishments, and a seemingly endless cycle of prayers and devotions to be performed over many months or years. […]
Despite popular notions to the contrary only a small percentage of cases concluded with capital punishment. The penalty of death by burning at the stake was reserved for three principal categories of offenders: the obstinate and unrepentant who refused to be reconciled to the church; the relapsed, those who had suffered a previous sentence for formal heresy; and individuals convicted of attempting to overturn such central doctrines of the Church as the Virgin Birth and the full divinity of Christ… if this is still not a pleasant picture, it is also not the unfettered violence which we may have been led to assume. To the very end every attempt was made to persuade impenitent heretics to reflect, to admit to the errors of their acts and teachings and seek reconciliation with the Church. From Giordano Bruno to the most modest prisoner in a provincial cell, it was the policy of the holy office to assail the condemned with the expectations of “learned, religious and pious” men hoping to extract a last-minute conversion.
In conclusion, although capricious arbitrary decisions, misuse of authority, and wanton abuse of human rights occurred, they were not an integral part of inquisitorial procedure, nor tolerated by the Holy Office. […]
It is impossible to condone coercion, the stake, and the other horrors perpetrated in the name of religion during the Reformation era. They were employed not only by the Inquisition but by virtually all other judicial bodies in Europe. In the 16th century they were an unquestioned part of legal proceedings. But I believe that future research will show that they were used less frequently, with greater moderation, and with a higher regard for human rights and life in the tribunals of the holy office than elsewhere. Skepticism and incredulity in regards to witchcraft invaded Roman legal circles between the end of the 16th and the beginning of the 17th centuries at a time when the land north of the Pyrenees and the Alps remained in the grip of witch-hunting mania. It was a modest step toward sanity, and a glimmer of hope at the end of a dark tunnel.
John Tedeschi, The Prosecution of Heresy (1991)