The Inquisition was the thing that troubled me most about the Catholic Church before I converted, and it still troubles me in a moral sense (but not from the standpoint that it disproves Catholic claims). I now understand much better, I think, why these things occurred, and what the Church has learned in the subsequent centuries. It goes back to the medieval mindset and worldview.
Unless one makes some objective attempt to truly understand that, they will never remotely comprehend the Inquisition or the Crusades, as the sort of motives which propelled the medievals are absolutely foreign to the modern relativist, indifferentist mental outlook — if not outright incomprehensible.
The Inquisition represented an expansion (compared to what we have today) in the types of “crimes” which were regarded as a threat to society (to include heresy). Therefore, it was a different — and yes, flawed — understanding of what constituted societal threats.
In the Middle Ages, all heresy was pretty much regarded as obstinacy and in bad faith; evil will, etc. The Church today takes a much more psychologically nuanced approach: much heresy is believed in good faith; hence the adherent is less culpable; hence not guilty enough to be punished, etc. (i.e., on the human level: divine judgment being something else altogether).
We have also learned that coercion is pointless, which was the original Christian position, anyway (before heresy became wrapped up in civil disorder, such as in the cases of the Donatists, Monophysites, Arians and Albigensians, among others).
I would submit that these beliefs constituted every bit as much of a threat to both civil society and the Church as, say, the sanctity of life and sexual purity threatens the sexual revolution and culture of death which we are currently blessed with. Beyond the strange, culture-destroying beliefs, the Albigensians were also less-than-saintly behavior-wise.
The medievals believed (with a great degree of justification from a Christian perspective) that heresy can be every bit as dangerous to individuals and societies as physical crime is (in fact, much more so, assuming the background premises). This inner principle has remained the same, while the application and particular understanding of it has undergone positive development.
The belief that heresy is bad and soul-destroying is altogether in effect today in Catholicism, just as it always has been. But the understanding of the motives of the heretic and thereby the treatment or punishment changed (along with the relationship of church and state in modern societies).
We can’t see today – as a society – the clear wrongness, injustice and outrage of abortion. At least the Church in the Middle Ages had a worthy motive for persecuting those they felt to be heretics. Right or wrong, the motive was to protect other souls from being led astray and possibly winding up in hell. That’s a far cry from the motive of sexual license without responsibility, or the monetary motive of the abortionist.
The killing of heretics was based on the notion that they were a menace to society, and would cause untold harm to society and souls, because in those days, heresy was considered as harmful and dangerous (if not more so) than physical crime is today. Humanists believe that the body dies and that is it. Christians believe that a deliberate, obstinate heretic will burn in hell forever; hence the high importance placed on preventing the spread of heresy.
I don’t think that the Inquisition can or should be absolutely defended by the Catholic apologist. I don’t try to do that. I don’t like the Inquisition at all, myself (since I view coercion in matters of religion and conscience as a contradiction in terms – precisely the position of Vatican II). But to say that there is no “essential” difference between the Inquisition and Communism or the Nazi Holocaust (as some critics of Christianity or Catholicism in particular try to do) is patently ludicrous and preposterous.
The Church has come to realize that the rights of individual freedom and conscience are relatively more important than temporal punishment of heretics (because the causes of heresy are regarded as extremely complex and not given to harsh and swift judgment).
Part of the reason the Inquisition is continually used as a reason to severely criticize the Catholic Church is a certain hostility toward the Middle Ages, which has become deeply ingrained in modern society. G. K. Chesterton made an illuminating remark in this vein:
There is something odd in the fact that when we reproduce the Middle Ages it is always some such rough and half-grotesque part of them that we reproduce . . . Why is it that we mainly remember the Middle Ages by absurd things? . . . Few modern people know what a mass of illuminating philosophy, delicate metaphysics, clear and dignified social morality exists in the serious scholastic writers of mediaeval times. But we seem to have grasped somehow that the ruder and more clownish elements in the Middle Ages have a human and poetical interest. We are delighted to know about the ignorance of mediaevalism; we are contented to be ignorant about its knowledge. When we talk of something mediaeval, we mean something quaint. We remember that alchemy was mediaeval, or that heraldry was mediaeval. We forget that Parliaments are mediaeval, that all our Universities are mediaeval, that city corporations are mediaeval, that gunpowder and printing are mediaeval, that half the things by which we now live, and to which we look for progress, are mediaeval. (“The True Middle Ages,” The Illustrated London News, July 14 1906)
Secularists have adopted relativism and concluded that, as there is no truth to be ascertained in matters spiritual and theological, therefore “heresy” is a meaningless concept. Civil punishment and even the death penalty continue to exist in civil society for crimes against properties and persons.
We can comprehend, I think, that the Church once advocated such penalties for persons who were guilty of crimes against the soul and spiritual truths, leading people to eternal hellfire.