Religion is a highly personal thing. I feel lucky to have parents that insisted I get some education in religion but always told me that after grade six it would be my choice of when and if and where to go to church. That I was a rational, thinking person and entitled to my own beliefs.
Is it possible that your youngest is not so much rebelling against the church or religion or the idea of God, but instead rebelling agains his dad? Your husband has pretty black and white views on religion, or did at one time, and I can see how your Youngest might rebel against his dad by rebelling against religion. Just wondered if that might give you some perspective.
I do believe that faith is on God's schedule not ours, and I think that might be a useful thing to hold on to for you.
If he truly wants to think all day, maybe he should pick a field of study, work his way through college and become a professor?? That is about as close to that as I could think of for him. He has an active, agile and interesting mind, and would be great as a prof, with some maturity and seasoning, of course.