Your son sounds like my husband as a boy. This is very much his story. He turned out quite all right despite being very bored at school until he got to college. He is a mechanical engineer and a wonderful person. Then, he was the weird, skinny kid, the geek, and did get bullied and beaten up a fair amount. He wasn't diagnosed with Asperger's until he figured it out for himself then got tested which confirmed his self-diagnosis. I think he was about 30 then. He is highly functional but still has trouble in social situation and with eye contact. Sometimes he speaks too loudly with too much enthusiasm for the comfort of strangers. He is self aware and works on it all. I just asked him. He says that he is happy.
He suggested looking into community college classes/summer programs for gifted youth. I was thinking something like martial arts which will help him learn self-control and about redirecting his anger and negative feelings into positive activities. It will give him a lot of self-confidence and self-discipline and of course will be great for him physically. You talked about controlling him. He really needs to learn self-control since you can't always be there. I guess we should ask how old your son is now, how old mentally, how old emotionally, how old physically?
Also, I learned with our own son, who is very bright and also very gay, he wanted badly to work out his own problems, with teachers, with bullies. It was often difficult for me to let him. It is in my nature to fight for him, fix things, try to make it all easier. He doesn't want me stealing his challenges and slaying his dragons for him. My son is 16 now. He is entirely self-sufficient, including financially. He recently got a full scholarship to a private college prep academy and has several small business ventures including ebay and etsy shops that make him spending and a bit of savings money. I'm very proud of how well he is turning out. Talk to your son about what he thinks he can do to better control his own anger. Ask him what he needs from you, from school, from his life right now. Best wishes to the both of you.