Historically speaking, there have been plenty of Popes who were complete assholes - there's a reason why a lot of Medieval art concerning Hell actually shows a number of Popes there.
How is the GM at showing other members of the religion? Is there a suggestion that the religion is the source of the problem, or is it just this one guy and his cronies?
I'm an atheist, but I got over my "rah-rah religion evil" phase a long time ago once I realized that a) humans are bastards and, if not for religion, would just find some other reason to kill each other, and b) for any terrible thing that religion has done, you can find at least one example of a good thing religion has done. It's positively affected the lives of millions of people. Who am I to deny them whatever comforts them, as long as they don't harm others pursuing it?
I mean, except Scientology. I reserve the right to still be an asshole about that.
My point is that if you feel it's a major problem, then just talk to your GM about it.
I was inclined to suggest this first, but I sense that if you do this then the GM might begin to feel that you're trying to "ruin his campaign". It's passive-aggressive, is my point.
Just talk to your GM like an adult. Maybe suggest to him, directly, that your character become a good not!Catholic to serve as a counterpoint to the evil not!Pope and show that even if the head of the religion is a dick, the religion CAN still do good.
Whatever you do, don't make it a personal religious debate, however - instead, just respond to any attempt with "I respect your views on religion, I'm just asking for you to respect mine and realize that your not!Catholicism is making me uncomfortable since it's been solely depicted as evil, and I'm just requesting that you allow me to play a character that displays its good aspects."
If he still tries to draw you into a religious debate after that and "convert" you to atheism, then abandon ship.