Well, again, it depends. What does "have to accept Alice as a girl" mean?
If they are being told they have to accept Alice in their changing rooms and showers and sports teams then yes, absolutely, they should be able to say, "But Alice is a BOY."
If they're being told they need to accept Alice in their friendship group which happens to be all girls, I think it's legitimate to say, "That's not how friendship groups work, we aren't being forced to include other girls in the group, so why are you trying to force us to include Alice?"
Or even just, "We don't want to."
Unless it is something relating to single sex spaces or sports I'm struggling to think of a situation in which the fact that Alice is a boy would be relevant.
I guess, at a pinch, if a girl has a birthday party and invites all the girls in the class to do a girly thing but doesn't invite Alice, that's a situation where I feel like leaving just one actual girl out would be bullying, but leaving Alice out because they want girl time with other girls and Alice is a boy is probably understandable. But do schools really get involved in things like this?