Reddit mentions of The Wrinkle in Time Quintet Boxed Set (A Wrinkle in Time, A Wind in the Door, A Swiftly Tilting Planet, Many Waters, An Acceptable Time)

You could try A Wrinkle in Time there is a nice 50th Anniversary edition, and a Boxed Set with the other books to choose from.

Some more YA books with religious figures and themes:

• A Wrinkle in Time, briefly, but generally positive
  
• His Dark Materials trilogy, definitely negative
  
• Good Omens, satire
  
• There's also the Left Behind crap. I hear terrible things about it.
  
• Speaker for the Dead and the rest of the sequels to Ender's Game deal heavily with religion (haven't read the sequels, but this was my husband's contribution)
  
  I think it's important to turn "trusted" figures into dangerous entities in YA fiction, whether that's by turning parents, teachers, coaches, and other authorities into antagonists or just portraying them as occasionally flawed people. While younger readers may benefit from some reassurance that authority figures can usually help them, teenagers are growing up and should be aware that questioning authority and the bases of their moral systems is important!
  
  You should cross-post this thread to /r/YAwriters. Looking for more discussion topics there, and I don't think everyone's subscribed to this sub.

Ok I thought of one more author: Madeline L'Engle. Beyond her A Wrinkle In Time series (<3 Many Waters <3), there's A Severed Wasp and The Arm of the Starfish both of which are departures from The Wrinkle in Time series but still great.

I'll throw another vote behind Good Omens if you're already thinking of reading it!

A Wrinkle in Time would be a quick read with religious overtones. It's technically part of a series, but it stands alone. I can't speak for the next ones.

Agreed, but i should mention A Wrinkle In Time is actually the first in a series of 5 (I haven't read the last four yet but they can be found here)

Yes! You can have it via Amazon Prime for $20! That's the one I have and it's pretty, though all the novels are paperback.

Here is a link to the books that I referenced.

http://www.amazon.com/Wrinkle-Quintet-Swiftly-Tilting-Acceptable/dp/0312373511