I'm hardcore when it comes to protecting children from the Watch Tower cult. There is no compromising when it comes to jws and their distorted world view. So unless you're prepared to tiptoe around the brainwashed mother, your husband must make a stand. Go back to court to get decision making rights for educational and medical issues. Have a guardian ad litem appointed for the child, and cooperate with the counselor who will inevitably be involved. If the system works, your husband will be able to determine whether his child will fit in at school by participating in holiday celebrations, sports, etc., as well as permit life-saving medical treatments that involve blood if the need ever arises. The counselor should be able to help the child with the guilt issues that his mother causes.
There are attorneys and/or consultants that specialize in jw custody matters. Your stepson's development is of the utmost importance, so it is worth any cost. By the way, since the Watch Tower's policies permit pedophiles to run amok in the congregation, your husband may want to have a serious chat with that poor little kid about the difference between proper and improper touching and assure him that he can trust his dad anything.