You can read about my recent Pope problems in the See Naples and die thread. The problem with taking out the Pope is that when he comes back, he comes back big time. There are usually 3 to 4 stacks in Rome and the Papal States and they are all good tech troops, all be it low valour. Even with a well developed empire they need a lot of resource to get rid of them. What is worse, they keep coming back. My advice, from bitter experience, is don't take them out until near world dominance - a sort of leave them to last approach. If you want to wage war on your catholic numbers either do it quickly or take the excomm. It doesn't last for ever and if well timed with an old King should only be a few years with no time for a crusade to be declared.