I'd be comfortable sending my son to Christian-based pre-k, though we don't because we have affordable secular alternatives in the area. I don't think a child's mindset becomes fixed towards one belief system at that age. I also would look at it as an opportunity to introduce my little one to a smorgasbord of religions. So rather than immersing my child in one set of beliefs, I'd take the time to talk about what other religions and cultures teach, maybe even taking field trips to temples, mosques and other places of worship. That'd help introduce the concept that there is a multitude of stories people choose from to either form their beliefs... or not believe altogether.
I find that pointing out the similarities between religions helps others reach a viewpoint that it all comes from the same (human) source. If you're looking for resources on comparative religion, Joseph Campbell's "The Power of Myth" is a good one, as is Huston Smith's "The Religions of Man".
Good luck with your decision, and I hope your kiddo gets some positivity out of whatever school you pick.
