I wouldnt exactly call this debunked. You have the statement by the school, who has an interest in this thing just going away. You have not heard from any parents as of yet.
If the principal did threaten these girls with consequences, do you really thing the super would not back the principal's play?
The Daily Mail did overblow the initial reporting (Fox is a 3rd level reporter, but hey, they are the preferred target so MM will make it seem they are the intial reporter to make them look bad) but there are still some base facts here. There is a transgendered boy using the girls room, and obviously there are people not happy about it.