Hi there Dr.Hasenbein

This has been discussed here before, I think, but I'll gladly answer it again, in short: You know, it isn't possible.

In length, the programmers decided it is vital for the Catholic factions to have a pope around, so you can do fancy crusades and sometimes get extra money from him,
so he will always come back. You could station huge armies in Rome so as to quell his rebellion as soon as it starts,
it can be done easily if you have a lot of money to spend and a relatively easy time beating the game. Just leave a good general there and you can autocalculate the battles.

If you don't want that sort of annoyance, you can leave him alone, or try making him retreat to the papal states or Naples or some other low income province. (That is, if you love Rome so much that you want it for yourself)