You know how JWs can't do anything the borg doesn't approve first? I think going would show that you are free now to do whatever you want. It will show him that no matter what he does, you'll be there for him. Your love for him is not conditional on what religion he is or what trouble he might get himself into at a later age. If you don't go, he might hate that you have different beliefs. If you go, you'll show him that no matter what your beliefs are, they won't stop you from loving him.
One more thing: If he got disfellowshipped one day, he'll say, "Uncle loved me no matter what. Now those people are shunning me."