I get your dilemma, MNNC. It is such a hard balance between taking a firm parenting stand and seeing your son become even more determined to study with this man. At your son's age, he is vulnerable to using anything you do as fuel for his own emerging beliefs. You so don't won't to drive him into their arms - yet you don't want to relinquish your parenting rights either. That's incredibly complex!
Many posters don't quite grasp the difficulty this poses for you.
Sure, you could 'up the ante' and find the household situation even worse. It is so hard when no one solution seems to consider all aspects.
I repeat what I said earlier: You need a safe venue for off-loading and being helped by an independent source to problem-solve and find a way forward.
Regarding your son's interest in the religion, keep in mind that many youth blow hot and cold with religion. He has his own right to decide what he believes and at the same time he needs to know that you are here for him whatever he believes. You love him unconditionally.
Another point, contrary to what the witnesses always say, time is on your side. There is absolutely no Armageddon emergency at work here.