I think, like @Joy said, it's going to take quite a bit of compromise from both sides.
On one hand, the site can easily go downhill from too many people shouting "omfg no religion!!!!!" and starting drama. Remember what happened to Paladore, anyone?
HOWEVER, if the site admins are too stubborn and refuse to change anything, and insist on pushing it into people's faces (i.e: a religious plot), they might as well be digging their own graves. As a user, one of the worst things a petsite owner can do is say "suck it up and deal, it's none of your business." They sure as HELL aren't getting $0.01 of my money, which is a driving force for many petsites.
On the religion thing, I originally joined KS with the sole intention of seeing how awful and religious it was with my own eyes. However, I was pleasantly surprised. I love the site now, and am getting ready to donate to earn some CS currency. I really am not too bothered by the prayer garden, but that's because I just don't go into that part of the forums.
Sorry if this is incoherent, I got like 2 hours of sleep last night, lol.