Women wear suits all the time. Men wear suits all the time. Lawyers, managers and other business people, attending formal gatherings, politicians, etc. Does the code at the school explicitly say that girls must wear a dress to their prom? No? Then they should have been admitted. Personally I think it might have been more a state of rite of passage for the teen - a statement saying "I went by your rules all these years and now I am an adult and can finally be who I am."
As a Christian school, it would have been more loving to allow the teen in, to show that they are not going to pass judgement on them as a person, and love and accept them despite their sexual identification. This kind of publicity actually contributes to Christian's own persecution and discrimination. The world hates us because we pass these kinds of judgements and they perceive that as self-righteousness, holier-than-thou, arrogant religious people that they want nothing to do with. And I don't blame them. But Christianity as a whole doesn't seem to understand the role they play in their own persecution, and then they (as a whole) whine that "the world hates us and treats us badly."
Where I live we have a Christian university that has rules - sex outside of marriage is unacceptable and they do not allow men in the women's dorms or women in the men's dorms. But they do accept students who do not identify as cis-straight, as long as there is no sex outside of marriage. The university decided to start offering a law program, but there was a big political and legal kerfufle about allowing law grads to practice due to the "discrimination" of campus policies. I'm sorry, but exactly how does this affect their ability to practice law???
In the same way, how exactly does a non-binary student wearing a suit to prom affect the student's status as a grad? As a grad, they have a foot out the door anyway... I say let them in and celebrate with them so they feel loved and accepted. Otherwise, keep them out and they will turn against the faith forever.