I'm very sorry tot hear about the bullying. However, re the school issue, if they take 120 presumably it's a 4 form entry and I'm sure wit ha quiet word you could arrange for him to be in a different class to the other boy.
I agree - with DD1's school, they were asked to say which children they'd like to be in the same class as.
Her primary that year had (very unusually) 11 girls going to the school, so they split into 3 x 3 & 1 x 2 (4 class intake). Then DD mentioned either one of twins from another school (as had they), so one ended up in her class. And there was a child appealing who got in after the classes had been allocated who DD had also asked to be in. A child from another school had put DD1 down on her list, as she didn't want to be in the same class as another child from her school...
Incidentally, I suspect that this year it will only be 2 or 3 going from that primary, but more shipping up to Cheltenham.
So hopefully, unless the school allocates classes by Surname, you should be able to give some option so they're not in the same class.