The bottom line is that this problem arises from too much emphasis on the boys committing the crimes being "trouble", suffering from "behavioural problems" and needing support. Quite possibly they do. But the problem is you cannot do this in the same mainstream school as the victims.
So you have to make a choice. Reintroduce reform schools/borstals, accepting that as a consequence many of these boys won't reform and will move straight on to the revolving door of the adult prison system, but make schools as safe as they can be for the victims.
Or say "no, we must look after these poor boys, because of course something dreadful must have happened to them to make them that way" (which indeed it probably has) - but accept that this is tantamount to saying "and screw the needs of their female victims, because girls don't count."
You cannot have it both ways.
Personally, I'm in favour of looking after the victims and reintroducing reform schools.