You're so young - I understand your hurt and confusion about what has happened with your wife.
Focus on you and your son. Your wife may try to erase you, but your presence in your son's life is make or break. I don't know if you have that expression there - but it's life or death. Especially since he's a boy - he needs you to be a role model for him. What you NEED to make sure WORKS is your relationship with your son.
I'm sorry the church situation is how you described. Are you sure there is NO church that you could attend for support? FYI - it's better for children to have religion in their upbringing than not. Children need to know to believe in something greater than mere humans.
I don't know - I've raised - am raising four children - and it makes a HUGE difference.