The newest episode of the podcast Clear and present danger – A history of free speach is all about the catholic inquisition, and it's very good. Highly reccommended.
Beliving that you know The Truth and that anyone lead astray from that Truth will suffer for eternity, how could that, combined with human greed for money and power, _not_ lead to atrocities? Of course it would, and of course God would know that it would, if he exists.