The Catholic Church was "wrong" about the inquisition the way Joseph McCarthy was "wrong" about the red scare. McCarthy was a nasty and self-agrandizing drunk but those of us who know the facts know he was right about communists infiltrating government, regardless of how the media has convinced the public otherwise.
The Catholic clergy at time resorted to cruel and overzealous measures, but they were right about crypto-Muslims infiltrating Spain at the time. I'd like to see what Protestants would have done if they had just taken back a country that had been under forcible Islamic rule for centuries.
Wrong is wrong. Why would I trust the interpretation of scripture to a fallible, human, institution which has alwasy done so in a manner specifically intended to enhance and increase its own worldly power?