The Narnia books are the ones that first come to mind. I first read them in 3rd grade; even at that age, it was pretty easy to recognize the allegory.
Slightly past your age group--- a high-school kid could handle Bujold's Curse of Chalion, so it might be close enough to look into, though of course there's more than just age/reading level that differentiates MG from other books. But she did a very nice job in creating a memorable religious structure and weaving it into her culture, so if you're looking for inspiration for your own project, it would be worth a read to see how someone else has done it well.