The thing about religiously themed books is that, unless the religion is one of many themes and there is a larger main plot, it might be best for the book to be marketed towards a Christian/Muslim/what-have-you audience rather than the secular market. If I were to find a book not labeled as Christian literature, and I read it only to find it chock full of Christian rhetoric, I would be pretty pissed if that wasn't what I was looking to read.
I agree wholeheartedly. I would be thoroughly annoyed to buy a book only to find out partway through that it was actually religious propaganda disguised as fiction. If I had bought it for my CHILD, I would be fairly livid.
(Now, I probably will read my children C.S. Lewis' Narnia series, but that's a bit of an exception to all of this. Partly because they're brilliant and magical, and partly because the Christian apology, while pretty obvious to adults, is cloaked in enough metaphor that kids won't see it.
The Lord of the Rings has some serious Christian symbolism too, for that matter, but again, it's subtle. If your religious symbolism is that well-hidden, you're fine.)
There's nothing wrong with writing YA Christian fiction, but you should market it as such. As far as I know, the Christian fiction market is thriving, so that's definitely a viable alternative. There's also nothing wrong with sticking some religious stuff into an otherwise secular story.
The example that springs to mind is the character of Michael Carpenter in
The Dresden Files series by Jim Butcher. Michael is a knight chosen by God to wield a holy sword against the forces of Evil, most notably a group of fallen angels whose souls inhabit the 30 pieces of silver paid to Judas for his betrayal of Christ. Normally, having all of this stuff in a book would make it Christian fiction...but Michael is a supporting character, and is stuck in among the host of other supernatural entities present in the books, including vampires, werewolves, fairies, Greek/Roman/Egyptian deities, and of course wizards. Harry, the main character, isn't Christian and has no plans to become one. Once in a while the Christian characters chide him about his lack of faith, but never once does it become a morality tale. The readers simply accept the supernatural Christian stuff along with all the rest, and it works. It's a delicate balance, though.