I had the same problem with Russia, but I executed prisoners very rarely and only when the captives were Muslims against whom the Pope had called a Crusade. This really shouldn't be a problem for the Catholics, so why the Hell do I have bad relations with every Catholic that is not my ally? I don't really have anything against Muslims, but they attacked me and I wanted to make a general with a Hatesmuslims trait so he's better at fighting them, as well as the invading Muslim hordes from Asia.