As you can probably guess from my post on your other thread, I would say that your issue is that you think this is an either/or situation.
The ideal, IMO, is "An opinionated child who knows their own mind, questions everything in their own mind, and accepts that they will be told stuff that they might not agree with, and be asked to do stuff that they don't like."
Honestly, I know where you are coming from with injustice. I still clearly remember an english lesson in year 10, when we were asked what we might find on a boy's dressing table. Being silly year 10s, about 5 of us shouted out "condoms", simultaneously. I was sent out of the room, and the other girls were simply told not to encourage me! Unfair? Yes. But, if I hadn't shouted out "condoms", the teacher would not have been able to go after me.
Just because I received a harsher penalty for the same behaviour as others doesn't take away the fact that my behaviour was unacceptable, it just means that my friends got away with it.
Your son needs to learn independence of thought which is satisfied by his knowledge and understanding. It doesn't matter if the teacher agrees with him, or if the whole class understands his point of view. He needs to be satisfied that he understands the topic to the level that he desires.
Also, I would go as far as to say that he doesn't need to have reasons for things to work out if it is fair. He wants reasons. But, he is 9, and at school the adult is the person who decides what happens. He needs to learn this lesson quickly, so that he doesn't have a frustrated school life (as I did).
I do agree with the other posters. In your anxiety to make his learning experience as good as possible, you are excusing bad social skills as being the complication of giftedness. Unless he is autisic savant, or has aspergers, (even then though, he can learn rules for situations with perseverance) he should be able to combine a healthy inquisitive nature with independent thought and a knowledge of when to do as he is told without question.