You used some smart and thought provoking questions. Continue to further critical thinking with your kid.
I am in a similar situation. However I told my parents how I feel about JW doctrines. I am also afraid to break my parents heart, but I think it is more important that they know my true feelings. They are sad when they think that I left, but they understand why now. We still have a very loving relationship.
When you want the indoctrination or bible study to stop,;you should really open up to your parents.
You will not stop all indoctrination as they will continue to talk with your kid about jehovah. But maybe you can tell them that they must stop "bible study" with him as this is not at all in their authority to do.
But don't be too strict, as you child is aware of all your actions. Most certainly further his desire to question everything.