I have no problem with any actor's person beliefs, provided that they don't attempt to force others to conform to their beliefs or go around acting as though their fame makes them "better" than the rest of humanity.
So, while I have no personal affection for Mr. Cruise, and no personal appreciation for his beliefs, I haven't seen a single example of him trying to tear down others, and I've seen a lot of people trying to tear him down.
Maybe I'm missing some super-secret cabalistic thing going on among Scientologists, but last time I checked, this was all voluntary. I think it's about the goofiest thing out there, but I'll defend to the very end the right of people to hold their own religious beliefs... until those beliefs start being implemented by force on other people, obviously.
I'm not the world'd biggest Tom Cruise fan, but I have no real problem with the guy, and I've enjoyed some of his performances.
My only issue with him being in this movie (unless he was unrecognizable) is that his presence would tend to overshadow the rest of the film. The movie already has one "big name" associated with it... that name being "Star Trek."
Unless he's the BEST POSSIBLE CHOICE for some role, I'd rather leave the "big names" out of the film entirely.