I would ask him about the possiblity of starting a self defense class, some sort of martial arts. Not so he can beat the other kids up, but to increase his self confidence and to give him a more controlled setting to meet other kids and maybe make some friends.

I wen to high school with a VERY religious guy who was shy quiet and the state's Golden Glove boxing champion in his age/weight division. Needless to say nobody picked on him and he NEVER got into any fights (outside of the boxing ring).