Well, Shambles, I was taught in a Catholic seminary that the Spanish Inquisition was a horrible injustice, an atrocity. There is (and was) absolutely no legitimate excuse for it. Certainly, we can seek to understand what led people to such atrocities, but that's no excuse. I have never come across a Church History text that has made any attempt to excuse or downplay the Spanish Inquisition. I have heard people point out that this was the Spanish inquisition, and not worldwide - but note that at the time, the Pope was Alexander VI, of the Spanish Borgia family.
For most of its history, the Inquisition was simply a church court - that wasn't the case in Spain in the 1490's.
-Joe Offer-