I think if you're going to apply to a schools that openly states its religious affiliations like Touro University, or Pikeville, then you need to think about what you put in there. If it's just a school with no particular affiliation, then I'm sure it's fine.
Personally though, I had one activity that I was heavily involved in from high school all through college and beyond, a very big part of my life, but I knew certain religious institutions would possibly judge it poorly, because it was slightly controversial, and so I actually left it out of my application. I do not regret doing so either. If your religious activities are controversial, like protesting abortion clinics, or whatever, then leave it out, however, if it's community service oriented, then you should totally put it in.