The Inquisitions are certainly a black mark on the history of the Roman Catholic Church. Jesus Christ advocated the forgiveness of one’s enemies. This was a radical position during His time as He carried this message into an “honor culture,” where the forgiveness of one’s enemies was difficult to understand (and is still a stumbling block for many in the Mideast).
In this light, the violence that occurred at the hand of those who claimed Christianity during the Inquisitions can be attributed to misguided individuals. They were acting according to the standards of the day rather than in a manner consistent with the teachings of Jesus Christ. These were unjust actions during an unjust time, and those identifying with Christ in their harsh deeds were way off course.