Conversely, does a young trans boy (ie, an FTM trans person) belong in an all-girls' school?
I don't see that this is anything other than reactionary -- and not well thought-through at that. The first point is that it frames all transgender people, young or otherwise, as potential threats, in a way that is grossly unfair and counterproductive. The second point is that, if the intent is ultimately to "discourage" people from being trans, it doesn't even achieve that. Adversarial attitudes tend only to drive people even deeper into whatever is prompting that reaction. The better thing to do is to provide a safe, open environment to explore these thoughts and feelings, and let people come to the conclusion themselves that it was, or wasn't, after all who they were.
If all we're doing is looking for ways to isolate, reject, ostracise these young kids, it's inevitably going to cause damage. Clearly you have to consider the majority too, but that can be done without penalising the minority.
This is Section 28 all over again, just with a different target. It was wrong then; it is wrong now.