Donohue quotes from an article by Dr Thomas F. Madden, associate professor and chair of the Department of History at Saint Louis University. The article is fairly long, so I've only given short extracts from it, but Maddern discusses how the Inquisition, especially the Spanish Inquisition, was not nearly as bad as purported in more modern times, attributing the latter's bad reputation to Protestant propaganda from several hundred years ago:
http://catholiceducation.org/articles/history/world/wh0075.html
One of the most enduring myths of the Inquisition is that it was a tool of oppression imposed on unwilling Europeans by a power-hungry Church. Nothing could be more wrong. In truth, the Inquisition brought order, justice, and compassion to combat rampant secular and popular persecutions of heretics...
Most people accused of heresy by the medieval Inquisition were either acquitted or their sentence suspended. Those found guilty of grave error were allowed to confess their sin, do penance, and be restored to the Body of Christ... Unrepentant or obstinate heretics were excommunicated and given over to the secular authorities. Despite popular myth, the Church did not burn heretics. It was the secular authorities that held heresy to be a capital offense. The simple fact is that the medieval Inquisition saved uncounted thousands of innocent (and even not-so-innocent) people who would otherwise have been roasted by secular lords or mob rule...
By the 14th century, the Inquisition represented the best legal practices available. Inquisition officials were university-trained specialists in law and theology. The procedures were similar to those used in secular inquisitions (we call them "inquests" today, but it's the same word)...
No major court in Europe executed fewer people than the Spanish Inquisition. This was a time, after all, when damaging shrubs in a public garden in London carried the death penalty. Across Europe, executions were everyday events. But not so with the Spanish Inquisition. In its 350-year lifespan only about 4,000 people were put to the stake. Compare that with the witch-hunts that raged across the rest of Catholic and Protestant Europe, in which 60,000 people, mostly women, were roasted. Spain was spared this hysteria precisely because the Spanish Inquisition stopped it at the border. When the first accusations of witchcraft surfaced in northern Spain, the Inquisition sent its people to investigate. These trained legal scholars found no believable evidence for witches' Sabbaths, black magic, or baby roasting. It was also noted that those confessing to witchcraft had a curious inability to fly through keyholes. While Europeans were throwing women onto bonfires with abandon, the Spanish Inquisition slammed the door shut on this insanity...
Madden goes on to write that the "Black Legend" of the horrific Spanish Inquisition developed as part of a "propaganda war" by the Protestants after the 16th Century CE:
Although the Spanish defeated Protestants on the battlefield, they would lose the propaganda war. These were the years when the famous "Black Legend" of Spain was forged. Innumerable books and pamphlets poured from northern presses accusing the Spanish Empire of inhuman depravity and horrible atrocities in the New World. Opulent Spain was cast as a place of darkness, ignorance, and evil. Although modern scholars have long ago discarded the Black Legend, it still remains very much alive today.
