You keep bringing up sex reassignment surgery for some reason. That is not a factor in this example.
I don't know the girls parents. I don't know the girl, other than seeing her interact around campus or in class. I do know that being a girl and wanting to identify as a boy is a pretty unique thing, and probably scary. This girl isn't an attention seeker, not a big personality. Obviously no one wants a child to be bullied, but it could have been met adversely by the student population. Kids could have kept their distance or thought she was weird. The opposite happened. I consider that to be a special thing, and I think everyone could practice a little more acceptance, and not see it as a "left/right" issue, as the original poster did.
To your core issue, I don't see these things as delusions I need to help them get over. I don't see this as an obvious psychological disorder. People felt this way about homosexuality, some still do. I'd find a professional for the whole family to talk to, and it leads wherever it leads.