Your son probably isn't going to be able to stop thinking and since a belief in God and heaven is based on faith rather than reason, it can be difficult to reconcile the two. You might talk to your son about faith and what it means. It doesn't even have to be religious faith. For example, you can talk about believing things to be true even when you don't or can't see them. Most scientists believe in the existence of black holes in the universe even though we can't see them. They believe in their existence because of the signs that point to their existence.
In the same way, many people believe in the existence of God because they believe in the signs that point to His existence. If your son likes science and/or math at all, look up the number phi (not pi). It's a very interesting number that appears everywhere: in art, geometry, math, life, the universe, and even in theology. Can it be the sign of a supreme designer? Learning about phi can give your son something to think about, even if he doesn't see it as a sign of God's existence.
You might also see if your son would be interested in George's Secret Key to the Universe, a children's book by Stephen Hawking. Hawking is arguably the smartest person since Einstein. He is certainly a brilliant scientist who ponders the nature of the universe, including how it got started. He is a believer in the Big Bang Theory -- and he also believes in God. He has an interesting perspective that I would encourage you to discuss with your son. Henry F. Schaefer has written a simple explanation of Hawking's views in his article "Stephen Hawking, the Big Bang, and God."
Hopefully, then, your son can see the most brilliant scientists on earth have no trouble reconciling a belief in God with the Big Bang Theory and also that some beliefs are based on trust. That is what faith is. Your son trusts you to take care of him. He has faith, not proof, that you will do it. He bases his faith on past experience, but that's not scientific predictor of what you will continue to do for him. That prediction is based on trust, on faith.
Hopefully, your son will find comfort from these ideas and from some professional help. It's not uncommon for gifted children to need such help at some point in their lives.