I think adding religion to Trek would be a really really interesting story line since it's really been largely ignored except for the Bajoran angle which wasn't all that interesting since apparently they only had one religion and everyone believed it. I think seeing a relgious person in the Starfleet would be a fascinating character to watch amongst a largely atheistic society.
That said, the reality of the situation is that we live in politically correct times where no one can ever be offended, heaven forbid, so it's better to just leave the drama off the table. Also, I think networks would balk at it too for fears of driving off viewers.