I my application, I listed my serving as a missionary for the LDS (mormon) church as volunteer/leadership experience. And, in my PS, I related a story from my mission where I learned about true compassion, etc. I also attended BYU (a mormon school), so I was asked several times about my faith, and especially whether how I would deal with people who were not of my religion.
I consider these questions fair game since my religion is such a big part of my life. I answered them honestly, and I since have been accepted to one of the schools that asked me about it.
Is it possible that my religion has prevented me from getting accepted from some school. I have wondered whether the LDS church's role in California's Proposition 8 has led adcoms at some schools to not offer an acceptance.
Bottom line, if you choose to be religious, especially if you choose to be Christian, then you have to accept that people are going to judge you, and persecute you. If a school is going to reject me for my beliefs, then I have no interest in going to school there. I would rather not be a doctor, than have to give up, or downplay, or hide something about myself that is such a central part of my life.