I will second and third A Wrinkle in Time, and the books that followed it (A Wind in the Door, A Swiftly Tilting Planet). She was an Episcopalian (she was the librarian and the writer-in-residence at the Cathedral of St. John the Divine in NYC), but I don't know if super conservative Christian parents worry about her or not - super conservative Christians don't tend to love Episcopalians. But I don't know if she's on their list. (I wonder how we could find out what YA books are on their hit lists? Do they make websites about them? They must, right?)
For the younger end of that age spectrum, I'd suggest some E.L. Konigsburg books. They are often about children discerning the rules that govern the adults around them, and figuring out their own truths (a wonderful example of this is Silent to the Bone). They often feature nontraditional families (like a brother and a sister making a family together in From the Mixed Up Files of Mrs Basil E Frankweiler). Stay away from the Jennifer, Hecate book because that's about witches. Outcasts of 19 Schuyler Place might not be good either.