Lots of stuff in the Inquisition was screwed up and yes indefensible as well. Was the whole concept bad? No, because (a) it was better than the civil courts of the time and (b) a lot of people wrongly accused were exonerated and spared from the punishment of the state.
I'm foregoing discussion of a lot of the aforementioned terrible things happening due to the secular power tending to overtake the ecclesiastical one's role. Nobody is going to say that there weren't evils committed by Church leaders during all this and I think that's where you are wanting to focus.
