It sounds as if your son was acting in self defense. However, the rules which apply in criminal law differ from those that apply at schools. Generally, schools have a "no tolerance" policy and punish everyone involved in any such incident. If your child is being bullied by the other kid, I would make certain that the school is aware of that situation. As you may be aware, the schools are beginning to take a hardline against such behavior. At this point in the process, though, I believe it is too late to further fight the switch to alternative school.
It's always said that the winner of the fight is the loser in court. Your son was clearly protecting himself according to your information, but decisions about who is at fault are usually made based on who looks like they suffered a beating and who doesnt.
My colleague is absolutely correct that there is a zero tolerance in schools and the laws that apply in the outside world don't necessarily apply in school. Instead of focusing on the self defense issue, i would share with the school board other information about my son, such as his behavior at home, demeanor with his family. Sometimes, we get very much focused on getting people to agree with us (that this was self defense) that we lose sight of what should be our argument (my son's a good kid, helps around the house, respects other kids, does his school work and deserves another opportunity)
Best of Luck,