Of course, all who wanted to play Klyros could go around saying 'bless this and that' and not mean it, but that just seems stupid.
Isn't that called roleplaying ?
I mean of course the player doesn't believe in any PS deity (or if that's the case, (s)he should get some help IRL ^^), but if his/her character talks and acts as a believer would, then there's nothing wrong with that. You can roleplay a character whose beliefs are totally different from yours, you just have to roleplay it consistantly.
Besides, I don't see a reason why we couldn't give some advantages to believers if that helps to maintain a good believers/atheists ratio. After all, a believer has to spend some time praying etc. and is restricted in his actions, so (s)he chould have some kind of a reward since an Atheist will have more time to do other things (working, mining, training...) and have more freedom of action.
Besides, the situation is different from the real world : IRL the gods either don't exist, or don't care about us, or interact with us through very subtle touches. As I see it, gods in planeshift interact more directly with the mortals, so it would be easier for a character to believe in them than it is for a player.