In my class last year there were two Muslims and both said that it didn't really affect their faith. When I went on a Philosophy trip to a university with my class, the majority of people from other schools were actually Muslim as well.
I'm doing A2 philosophy, and a lot of the course is geared towards forming your own arguments, so even though you do learn about criticisms of God and religion, you can always use counter-arguments that support your personal beliefs. Even if you do want to argue from an atheistic viewpoint, you don't necessarily have to support it. I generally always argue from an atheistic viewpoint as I find it easier to critique things rather than support things, regardless of the actually argument.