Avenalife, I have to say that I have often read your threads and thought that what your son needs more than anything is a firm set of boundaries regarding social boundaries. Please don't think I am being critical, I am speaking as a former child-who-saw-the-injustices-of-the-world.
I was a bright kid, possibly not scarily, as your son, but I was assessed as having the IQ of an 8 year old at the age of 2.
I remember finding it impossible to accept the injustices that presented themselves at school. For instance, why was I made to do art when I was clearly much better at maths. Other children were allowed to do maths while I had to do art.
I was very unhappy at secondary school, and had frequent disagreements with my teachers, because they were often hypocritical. A clear example being the head teacher berating children for wearing make-up whilst wearing the whole of a maxfactor counter. Or the teacher telling a girl off for having a little necklace on, whilst jangling 10 bracelets on one arm.
I was bored at times, but actually what I needed was to realise that sometimes life isn't fair, and that there is a difference between your personal viewpoint, and your behaviour.
Your son can wholeheartedly disagree with a teacher's point of view, and when he gets to Uni it will stand him in good stead. But until then, he will have to learn that there is a time and a place for his opinion, and that he has to learn to show respect to his teachers in class time. Whether he actually FEELS respect for them is irrelevant. (I personally think that respect is earned, not deserved) He has to learn that there are times when he has to button his lip, put his head down and do his work.
It won't do him any favours to wait until his adult years to learn that there will always be someone with more authority than you, and that you sometimes have to learn a bit of diplomacy.