I dunno, according to the second site (not 100% unbiased looking) intersex births are somewhere around 0.05% of population (1 in 2,000). I'd be amazed if 1 in 10,000 actually applied to legally change their gender.
Anyways, by the article:
people born in the city would be able to change the documented sex on their birth certificates by providing affidavits from a doctor and a mental health professional laying out why their patients should be considered members of the opposite sex, and asserting that their proposed change would be permanent.
It's not just John Doe walking down to the DMV and saying he wants to be Jane Doe. Assuming that the Board of Health actually reads and considers the doctor's affadavit rather than just rubberstamping all of them, and has some written standard for the hows and whys of the change, I don't see a problem with officially changing a person's gender.