Maybe I am for too much confrontation, but I think it is important to lay down some boundaries (privately) with the mother. With your husband, you need to tell you that while you are not ever going to disrespect what she does with her son or how many meetings he attends with her, FS, whatever, so long as you feel he is safe, you expect that she respects that his time with you is his time with YOU. You are not an extension of her or her lifestyle. If she thinks she can control everything, you might as well give up custody altogether.
You can't give him back the time wasted on the WT when with her, but you can give him a normal childhood with you. And I think if he wants to play soccer or baseball, then he SHOULD, (and join scouts and choir and the marines if he wants to!) and tell her that if she wants to ruin his time with you, you will seek counseling for the 3 of you so that she sees that her actions are damaging. Point out that YOU were to do what she does, and try to ruin every JW activity by guilting him out or making him see how stupid it is (might want to be more diplomatic, there) , you would be no more guilty than her, but the child would be utterly miserable-that is what SHE is doing to him by undermining his time with his father and you. She needs to keep her JW influence to herself and not impose it on you and his time with you. Which means that if his visit is on a holiday, he celebrates without her saying SQUAT about it.
Take it to a counselor so that the child is protected, but don't let her run YOUR life and control YOUR parenting of the the little boy. What you have said already sounds as if she is damaging him and that is wrong-she should not be allowed to do that.
This is the unlearned, but experienced voice of a 25 year veteran of mommyhood. Don't screw it up for the kids!