I had a problem with this in Dragon Age. I'm a staunch atheist IRL, and I was trying to RP a character close to my own personality. Naturally, I disagreed with Liliana a lot, and sympathized with Morrigan and Sten. Then there was that magic urn quest. I mean, Sten and Morrigan just kept criticism deity worship and denying the efficacy of these little relics within a breath of shooting motherfucking lighting at people. I talked to the actual spirits. The relic worked. And they still played the part of the skeptic. Now I always remember to look for evidence specific to that universe before I make a call about my religious views.