I don't think my DS is "quirky and original" and it says a lot that you are this defensive over your son. It doesn't help him in the long run.
But he has many attributes, as well as many things that I can be honest about, that prevent his peers from liking him. Whilst I love him, I have experienced many a day where I dislike him greatly. I'm the person who loves him most in the world, and some days, god knows I could merrily leave him to be raised in the woods by wolves. As for this situation....teen peers, who have to spend all day in class with him, then he follows into lunch each day and they've done their best to involve him, but their patience has reached it's end? On their behalf, I get it. So should OP. It sucks. But it's not the place of one peer group to "fix" because that's the one OPs son has chosen to attach himself too, and they can't say no because "bullying" 
I doubt very much that he's simply sitting their quietly, eating his lunch then leaving them alone. I expect much more that he feels over attached and familiar after a classroom conversation about cars with one boy within the group. Perhaps he is repetitive, trying to start conversations about cars all the time, as that's all he recognises has worked, once, before. Perhaps he really encroaches on this one particular boy, who has no interest in OPs son, who simply happened to have a conversation about cars in a science lesson, once, long ago.
My point is, I have a non NT child, and I know what they can be like. It's not their fault. But it's not the other children's fault for becoming exasperated, then projecting that they are unkind, mean, etc. This isn't about non acceptance, or bullying. He's been attaching himself to them, uninvited, for some time, and they've accommodated....and now reached the point of enough. Without malice, they've said that they don't want him to continue doing this.
This absolutely shouldn't be forced. It's not how the real world works. Not everyone likes you. More people don't like non NT people, sad but true, and it's far better helping them overcome this, than fighting it. You won't win. You can't change that. I truly believe you are teaching him the wrong lessons, and it seems quite a few other non NT mums on the thread agree.