Okay, some of this is reacting to my own experiences, not directly your post BUT -
The bully isn't picking on him because he calls out in class. They are picking on him because he is different. I quote: "One cannot blend into a crowd if the crowd is so different from oneself that it is not camouflage. It's like trying to hide an elephant in a flock of chickens by telling the elephant to squat down and cluck a lot." (
http://www.grcne.com/divergent-thinker.html) Telling your son to not call out is like telling him to squat and cluck a lot. It really isn't going to hide him.
Sorry. If only it was that simple.
(That doesn't mean that telling children not to call out because it is rude isn't a good thing, or learning social skills isn't important, BTW.)
I can't give much advice, I got out of the situation by leaving the school, but that may not be possible or necessary in your case. But I would certainly not be happy with the school trying to turn it around. That is wrong. And I personally would be after specifics about HOW IN DETAIL, they are planing on "Addressing the bully" and how they are going to measure success. Also what plans do they have for what your child is supposed to do if the bullying continues? Are they going to address "By-stander behavior"? (some of the more effective methods of reducing bullying include that)
IF you get a psych with good skills and knowledge of gifted children, it could work in your favour. Otherwise, maybe not.