Just because it's different or not what you teach doesn't make it bad or wrong. If there were only one way to teach hitting then every single hitter at every single level of ball would look the same. It's not that way.
That being said I'm not a fan of the "it's only going to be done my way" philosophy. I pretty much teach what you described the AA guy was teaching but I have seen the other method work. So if I got a guy who can hit using that method then I'm going to pencil them in and tell them how great they are.
Your son is going to have to learn to deal with different types of coaches and teachings as he goes through this game. Some of it's great and some of it's terrible and some of it won't make a lick of sense. Doesn't really make it wrong. Plus, if something is changed it won't feel "right" to the player on the first try. He has developed a habit (good or bad) that he is used to. Any change to that habit is going to feel uncomfortable. It doesn't mean they should stop trying to make the change if it's good for them. It's like riding a bicycle - you don't just hop on one and start riding it. You have to learn how to ride it and that takes time.
I got a player right now who drops his hands when he hits. Obviously he is not doing very well right now. I got him doing a drill everyday that is helping but he's still dropping his hands although not as bad. It will probably take another week of doing that drill before it becomes a regular habit for him. We got to keep working at it and make the change. If we quit after the first time trying the new drill he would never get better.
You said your was an average hitter - to me that means he can improve (of course you can say that about everyone). He might pick up something in the new style the JV coach is teaching that will help him.
Teach him to cope with what's going on to make adjustments. I realize you are on here pretty much just venting and there's nothing wrong with that but think of this - if you go to the coach and say anything (even if you mean it positively) do you think he will change? I doubt he will.