I agree with Oubeliette. Imagine that you were still a believing JW and your wife was Catholic. Would you allow a priest to indoctrinate your son into the Catholic faith against your wishes? Would you meekly accept it when he refused to even discuss it?
I know it's hard, but you must stand up to these clowns. It's hard because you have been conditioned to meekly accept the authority of the elders. Even when you realize it's not "The Truth" you are still being affected by the mind control and they still are exercising authority over you. They only have the power you give them.
Tell your wife that if she is not respecting your headship and it needs to stop. Personally I think the headship thing is nonsense, but supposedly she should still follow it. Tell her you will study the bible with your son and use that as an opportunity to counter the Watchtower indoctrination. That way you can help him see the Watchtower is not following the bible.