I think it is kind of a matter of things going from one extreame to another before we grow as a society, and stabilize. People have been put into rolls, and expected to be what they are not for so long, and to an extreame, that now to break out, things have to go extreame in the other direction.
There will undoubtably end up being cases as you are suggesting this may be. It is sad, but it is part of growth. There will always be those that struggle when we make progress. It is progress that needs to be made though.
Hopefully this will end as a happy story, where two people are able to live life as themselves, and not bare the burden of living in a disguise that fits a broken society. They already have the support of their family, and that is huge for anyone.
It will be nice when this is no longer a news story, and we get past this whole boy vs girl vs transgender, straight vs gay vs bi, long hair vs short hair, dresses vs pants, pink vs blue, trucks vs cars, dolls vs games, and all the other ridiculous things people come up with to say who or what you are, or are supposed to be.
This isn't an issue about acceptance at all though imo. If they were adults not being recognised by society as male or female after they'd gone through surgery it would be, but they're not and it's not; they're currently young children, not even teenagers, let alone fully grown adults, and they're about to make irrevocable life decisions (the first kid is going to be put on hormone blockers, to prevent her/him going through puberty) and are on the path towards gender surgery. Both of them.