I don't know you "MNIONC" and I can only draw conclusions based on what information you have provided. The fact that this situation has gotten this far out of control, coupled with the statements you made about your wife's authority over you and the "system being stacked against you", leads me to believe that your family dynamics has been askew for quite some time. I don't think this happened overnight. It seems like you see yourself as a victim rather than as one half of an equal marriage .
You have as much right as a Father to have a say in your Son's religious upbringing as your wife does. Jehovah's Witnesses think they call all the shots and are above the law of the land in these matters and are used to carrying on as such. You as a former Witness, are also used to allowing them to have control over you. Being freshly out, you probably have some residual brainwashing left over. You are behaving as if you've done something wrong or should be ashamed of yourself. This is often how former Witnesses behave at first.
I would find out PRONTO what my exact legal rights as a Father are in this situation and exercise them to the fullest. Once I had my ducks in a row and completely understood where I stood legally, I'd let this "brother" know in person, calmly and in no uncertain terms, that he'd better back off. Don't ask your wife for permission...in fact don't even tell her you're going to do it. Did she ask your permission when she hired this interloper into your family affairs?
Just Go ! If he refuses to talk, notify him via registered letter from yourself or from your Attorney, that he'd better stay clear of your Son or be prepared to face legal consequences if he doesn't. I can't imagine my wife ever granting me "permission" to do something or telling me that I'm "not allowed" to speak to someone unless she say's so. Doubly so when it comes to supervising my own child. Nor would I ever do that to her. I can't imagine how you could have written that sentence about her not permitting you to talk to that "brother", and not seen the entire basis of of this problem, but maybe I've got the wrong take on the whole thing.
In any event, I feel for you and I'm glad you presented your situation here. It's going to take some quiet strategy on your part, to turn this around to the point that you are on equal footing in this matter. Depending upon how all of this goes down, your wife may have a newfound respect for you in the end.