From my personal experience, I would encourage you to let your son make his own choice regarding church, especially if he is being respectful and filling his life with other positive things. I was very religious as a teenager, but now that I'm an adult I have done a lot of heartfelt searching and thinking and have come to the conclusion that I no longer believe in the religion I grew up with (or any religion at this point). It completely devastated my parents and has been one of the most painful things we've all gone through. I hated disappointing my parents, but I have not rejected morals even though I have rejected religion (I consider myself agnostic). My mother's initial response when she found out was to cry herself to sleep for 3 nights in a row. I love my mother's email to me after she found out and I encourage you to take a similar approach if maintaining the relationship with your son is your priority:
"Dearest Daughter (and Son-in-law too), I'm writing this letter to make a confession and an apology. I'm choosing to do so via e-mail rather than in person, because I feel I can be more fluid in writing. A few months ago I asked your sister about your "church" activity. It was totally wrong of me to do this and I promise you it won't happen again. I have not, nor will I, discuss your feelings with anyone else. So I ask that you please forgive me. I love you both so very much and I realize I need to show you more respect. I know I can sometimes be rather persistant regarding my opinions, so I will try to be more considerate and sensitive. I have complete confidence in your personal goodness, your wisdom, and your desire and ability to discern truth. I appreciate the wonderful marriage you have, your devotion to your children, your self-discipline, your integrity, your kind service to your siblings, and especially your goodness to me and your dad. I don't ever want you to feel ostracized or criticized for what you do or don't believe. My whole goal as a mother is to lift, encourage, love, and serve all of my children as best I can. Please be patient with me as I continue to learn. With all my love, MOM”
My email response:
“Mom, Thank you for the sweet email. Apology accepted :) Thank you so much for your willingness to be openminded. I really appreciate it because I know this must be hard for you. I must admit that it's a very uncomfortable topic, and reading your gracious email was quite a relief. I was pleasantly surprised and impressed. You still love me! It's not conditional :) Thanks for clearing the air a little. I think there's not really much to discuss regarding the issue and that not much productivity would come from hashing things out, but I do think that a mutual respect for each other's beliefs is the best approach.
To quote your email--"My whole goal as a mother is to lift, encourage, love, and serve all of my children as best I can." I just want to assure you've done an exemplary job of meeting your goal. Thank you for your confidence and respect and understanding for me and DH, and thank you for all the help you offer and give to make our lives easier. You are such a sweet mom and have such a good heart. I wish everyone was as lucky as I am. Please know (as you already pointed out) that DH and I have a wonderful healthy marriage that brings so much joy to both of us, and that we are earnest and sincere and no matter what will be good people that you can be proud to call your children. I love you!"
I wish you luck as you navigate this difficult, confusing territory.