What's actually super interesting about the kid's comment is that while clearly written by a clever kid, he specifically never states that he is too smart for this, and that seems intentional.
It seems very much that the kid recognizes that the system is flawed, and not that he is too extraordinary for the system, so in my opinion, trying to appeal to him in the: "If you were that smart you would've just finished it next to all your other stuff." sort of manner will be of no effect.
Now, I don't even know if I think he should stick around through school, I likely would not have, but if that's what you want to argue to him, I'd suggest that the best way to do that is through showing him how non specialized education is helpful all through life, which I argue will be very difficult, because we have an educational system that stresses specialization over a more liberal education, and I think he recognizes that.