I'm assuming this is the same son, and perhaps the same friend(s) you have written about since last spring.
It's very hard to see our children hurt and upset. We all get that. But if I understand you correctly, your son threw a toy and hit someone. You say it was an accident, and maybe it was, but how come your child is this age and cannot control his urge to throw toys? Your son also participated with the "problem child" in teasing and bringing another child to tears. Yet you say your child is "soft" and "very sweet" and "kind." You blame the child he follows instead of your own child, as if your child is helpless and blameless, and the other child is the entire problem. Really? You say your child is "shy" and is "so comfortable" around the family friend. Perhaps your son is comfortable because this friend is a willing teammate, not purely the instigator, in engaging in activities like toy-throwing and incessant teasing.
You also say there are "many incidents you hear about" - from whom? From your child? Form an objective teacher or school employee? From another child's parent who may have a bias or a horse in this race? Why are you basing your opinions on hearsay? Why have you decided that your child is a pawn and always a sweetheart? There was an old TV show, "Leave it to Beaver," which featured a character named Eddie Haskell - a kid who always was sweet and polite to the adults and then was a sneaky, rude guy as soon as the parents' backs were turned. He was a teenager whose parents never intervened or looked objectively at the situation when he was 7. Think about that.
You keep writing about what to do, and yet the problem is continuing. I think you have to look at your own starry-eyed view of your child, first of all. If you are working with a child psychologist, that's a good start. Your child may have issues with impulse control and reading social cues, or he may need a much firmer disciplinary style than your "poor shy dear" attitude. I don't know. I do know that this situation is untenable for your son and for the other children around. So I think you ALL (yes, you too) must work with this psychologist. Please stop filling the therapist's head with only your view that your innocent sweet baby is being manipulated, and be open to allowing the therapist to assess things. You'll never get anywhere in counseling if you decide up front what the problem and solution are.
If being with this other family is a bad idea, accept that friendships run their course and stop hanging around so much. If you truly love the parents, go to dinner and a movie but leave each kid with his own sitter. However, if these people are the terrible parents you imply they are, with a cruel child who also leads your child into the valley of evil, then I don't know what you have in common with them. Certainly not basic values. Maybe you should cut ties and refocus.
Otherwise, I think it's wise to let children work out their own friendships, and reap the consequences when they make poor choices. Poor choices include throwing things, hurting others (physically or emotionally), being a bully who teases over and over, and continuing to choose friends who are not a good mix. Your son may need to be disciplined by the school, miss recess, get sent to the principal, and be grounded at home - but that means you have to accept that he is responsible for his actions. It's really okay for kids to pay the price for their poor choices - whether it means being disciplined, feeling peer pressure and shame, having hurt feelings, and missing out on things because they did a bad thing. Please don't be a "lawnmower" parent who tries to mow a clear path for the child, removing all obstacles from their path. Bumps in the road often teach us far more.
ETA: I read your SWH - important details there that would have been SO much more helpful in the original post. So for example, if the toy he threw was a Frisbee, that changes things! A Frisbee is designed to be thrown, so this is more like a kid getting hit with a baseball or football. These things happen. BB hit your son in the head for that? BB is the problem. I'd cut back contact, ask the school to put them in separate classes (which I realize cannot happen until next year), and start play dates with other kids. Your son is afraid of BB yet won't break contact or stand up for self/others because of that fear. That's what you get professional help for.