Part of this sounds like a normal stage of growing up. Your son is nine now and becoming more aware of the differences between Autistics & NTs, and also the way NTs can treat Autistic people. Keep talking to him and if there's any sign of him being bullied at school, talk to his teachers/school staff about it.
I also think the X-men comics are a great idea. I always loved the X-men because they were not "perfect" super heroes, but heroes with real problems. I identified with them.
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?No great art has ever been made without the artist having known danger? ~ Rainer Maria Rilke