As a follow-up to the post detailing some “myth-busters” involving the Crusades, some interesting information can also be gleaned about the Inquisition, its most famous manifestation being that which occurred in Spain from the late 1400’s until 1808. Like my previous post, I will avoid (for now) getting into the theology involved here, and will instead focus on the historical events and politics that demonstrate why the Inquisition occurred.
The first item that we need to try and understand is that there was no such thing as “separation of church and state.” To divorce the two is a post-Reformation, post-Enlightenment idea that still is debated in modern society, even though the general populace has accepted the idea. Also important is the idea of “community values” as opposed to the more individualistic mindset that we have today. With this in mind, several points can be made, via J.P. Holding at Tektonics*:
1. The Inquisition arose because of social survival. “Stalcup notes that the Catholic Church (CC) in the so-called Dark Ages “was the one stable institution that provided leadership and order” and quotes historian Bernard Hamilton as saying that “as the sole vehicle of a more civilized tradition in a barbarous world” the CC “became involved in social and political activities which formed no part of its essential mission, but which it alone was qualified to discharge.” 
2. “With the exception of a few Jews and Muslims, all people in Western Europe depended on the CC for meaning and survival. Any undermining of this social construct was a threat to the physical, mental, and spiritual well-being of the whole. Kamen likewise says of the Spanish variation, “It fulfilled a role…that no other institution fulfilled.” [K82]
3. In Spain in particular, there was great unrest because of the “reconquest” of Spain, in which the Muslim invaders had been finally thrown out, and periods of civil war ensued. The possibility of spies or fake converts was very real, and since faith was an integral part of culture and government, any sort of heretical teaching would seem even more dangerous, because one might be a “closet Muslim,” a.k.a, an enemy of the state. One can easily see why the Inquisition persisted in Spain. It is also important to remember that Islamic armies were still a threat until the important Battle of Vienna in 1683.
4. The justice system, interrogation methods, etc…while cruel and unusual by today’s standards, were very normal practices during the day, and actually BETTER then the state managed counterparts. This doesn’t justify the behavior of course (especially the torture), but we would be foolish to divorce such practices from historical context.
Again, I am not endorsing or commenting on much theology here, but instead demonstrating that by the social standards of the day, the Inquisition is understandable, and actually demonstrated a level of restraint at times. And like the Crusades example, even if there was some malevolent plot in which evil clergy were going crazy, it has no bearing on the veracity of Christianity, but only demonstrates the human nature of any person in power, church or state. If anything, this demonstrates humanity’s need for the Christian worldview, and one shudders as to what may have occurred if the state religion was atheism (Oh wait, I remember there was a guy named Stalin…).