My first thought then though is that that's an argument against using, or requiring, a birth certificate as ID.
Problematic as it certainly could be, it seems to me that this ruling is fundamentally correct, since a birth certificate is not a record of a person's identity over time, but of their identity at one and only one point in time - at birth. Not just in this case but in all cases, it would seem that the idea of updating a birth certificate is inherently flawed.
Possibly the best solution would be to omit information about sex from birth certificates entirely.