You're my hero. And this is a prime example of why.
It's always been my philosophy that I will live my life, respect theirs, and always leave my door open, even if they close theirs.
I know this has to be hard on you, but I also know you've given it plenty of thought as well. Give it a few years, somewhere around 18-21 will be the real testing of if he sticks with it or moves on. A lot of times it takes actually being baptized and all that goes with it to fully get how messed up it is. If he has even half of the curiousity and reasoning skills of his uncle I think it will all work out ok in the end. Especially with you there providing that prodding and comforting at the same time.