I took rome as a Catholic nation and just made sure to kill the pope before he could hire Mercs.

Just so you know, you can send a diplomat to the the pope stack, and if you offer him one of your regions (like..Rhodes..lol) he'll suddenly forgive you and make peace. After he dies, all other popes will appear in whatever region you gave. So be sure to give him a region on the edge of the world. Timbuktu might be nice...