MouseWife, I would definitely say from what you've posted so far, I admire how you're handling it. The important thing isn't what YOU feel about it, it's what HE feels about it. You seem to be letting him ask the questions and search for the answers himself. That's the absolute best thing you can do. All you have to do is let him know that he's free to think about it any way he wants to, change his mind about it as much as he wants to, and come to any conclusion he wants, as long as he continues to treat people who've come to different conclusions with respect.
As you might imagine CP and I have spent a lot of time on similar subjects. We've been finding
Parenting Beyond Belief and
Raising Freethinkers very well thought out books.