I could not stop thinking about your question while I completed my morning routine of breakfast, pack lunches, get kids to school on time...
You are not alone at all. I have many religious (Christian) friends, myself included, whose children have chosen the exact opposite of what they were raised with.
I cannot for the life of me remember the name of a phenomenal book I read years ago when oldest daughter, now 22.5, was small. It was something about what NOT to do as a parent, rather than all the common parenting books of what one should do.
The psychologist couple who wrote the book were well known and established marriage and family counselors in the Mid west. Their combined years of practice exceeded 20+ years at that time.
Their premise, based on all the common issues they witnessed, resulted in a book of what people who sought therapy, mostly complained about. And a book about how to raise your children as to avoid these huge emotional conflicts later in life was born.
One of the recommendations was, that it is important to pick a religion, any religion, to provide a spiritual anchor later in life. Too many adults came in hopelessly lost, searching for purpose in this life. The adults who were raised in a free for all, you can choose for yourself when your older home, don't necessarily fare well spiritually later in life. The end up resenting their parents for not providing that structure and struggling without faith to carry them through.
I don't know if this fits with your particular circumstances. But it is what you happen to mention in your post, the religious choices of both how you raised your son and what he has ultimately chosen. He chose structure and ultimately an extremely organized church with dogmatic teachings and very black and white instruction as to whom is going to hell and who is going to heaven and there is little wiggle room.
He might eventually see through the judgemental teachings and learn to be more accepting of your choices.
It might help for you to show some interest, even at an educational level, of why he chose this path. There are many classes available at churches for 'non-believers.' There is no pressure to convert, just to educate. One is called the Alpha Course. It would help open that dialogue between you and perhaps bring you closer.
One more thought, is he at all threatened by you? Would he feel that you would disagree with his adult choices so he doesn't want to go there with you?
I wish that you both find a bridge.