No need to second guess yourself or rationalize why the school placed him with the "bad boys" at school. If you feel like this classroom arrangement isn't going to work for your son's temperament, I'd start working on getting him placed in a different classroom now. If the school gives you trouble, I'd have a second plan in mind such as an alternative school that might be more supportive of your needs.
I personally do not see any value in forcing your son to suffer through an entire school year with a group of kids he's not compatible with. While socialization is important, so is mental health, and most important of all whether or not he's in an environment where he's able to learn to the best of his ability.
Considering you do live in a small community, you have the advantage of knowing these kids,and probably their families too. Trust your intuition and do what you think is right for your son. If you think these kids are bad news, you're probably right. Clearly, the experiences you and your son have already had with these kids must have been pretty bad, and clearly you weren't happy with the support you recieved from the school, so be proactive and be so guilt-free! Forget the second guessing your feelings, or apologizing because your son is probably more advanced emotionally than these kids who are bullies. You know him better than anyone, and as his mother you probably know what he needs to thrive and be the best that he can be.
Besides, I don't think your son will miss out on some sort of "learning moment" if you don't put him in a situation where he'll have to fend for himself everyday. If left to defend themselves, most kids become bullies themselves, and rather than develop coping skills, instead develop serious mental problems that can lead to violence or other alarming results. While in your case this may be a stretch, it is more likely he could go through a very non-productive academic year because his self-esteem may dwindle, depression may set in, or he'll just develop an intense dislike for school. What's the point of that? Bullying is a terrible problem, and sometimes the only way to fix the situations is to take the upperhand before things get out of hand. And if the school is putting him in a classroom full of troubled kids to help set the pace...how awful. That IS like throwing him to the wolves!
You do know what's best for your son, not the school. If you know he'll do better with another group of kids or in a different setting, then he needs to be with the other group of kids. Don't be afraid to go head on with the school. Fight for his needs. This isn't teaching him avoidance behavior, this is just you doing the job of getting as many chips in his favor.