It seems that often with kids, the more you fight against something, the more it intrigues them. I wouldn't worry too much about the Superhero craze; it does seem to be normal. After all, most kids are exposed to such quite repetitively.
That being said, you could try to limit exposeure to the devices your child accesses it on, like TV, or game systems. Set up certain times for it, and certain times not for it. Personally, I wouldn't pick on books, though. You should be happy the child is reading!

Maybe instead of focusing on the violence, you could focus on some of the character's good qualities. "Its nice that [Superhero] wants to save the world. What are some ways we could help?" Or "[Superhero] is such a nice person, its a shame [villian] isn't willing to talk things over so they can be friends. Do keep in mind that while peace is always the first option, there will be instances in where parties involved won't feel the same as you, and you might have a violent situation on your hands. You could also talk about what you'd do in times like those.
Mythology can be a good teaching tool. There are alot of myths in various cultures that can be made child friendly, and many lessons to be learned from them. They might appeal to your son, if you can pick out some of the more "superherolike" characters. Some are easy to find(hell, Marvel seemed to have borrowed Thor), others you may just want to present to your son and see what catches his fancy. I'd work from his tastes; my own son is fascinated with Medusa, and we've had some talks about anger(he has quite a temper), and what happened to Medusa when she saw her own angry, hateful face in the mirror. It stuck with him.
I hope you're able to find a balance that makes everyone happy!