What bothers me about gifted programs is that they isolate the smartest kids from everyone else, and one can't help but think it's more to protect the system and everyone else from bored intelligent kids than to enrich their individual educations. IQ isn't a great proxy for much, but two or three standard deviations from the mean in populations of millions, you are likely dealing with different kinds of thinkers.
The skills the programs emphasized are focused on abstraction and complex problem solving - and not leadership where they could scale to benefit everyone. This turns kids into talent who will ultimately work for and be managed by more average peers, which makes it a remedial program for socializing exceptional kids into functioning cogs. It's like inventing fusion reactor to plow fields, or an F1 car to sit in traffic. I get that enrichment in education is something they might not be able to get at home and the schools are providing it, but they're providing what the average of the education bureaucracy can be persuaded is right for smart people to do based on cliches about scientists and professions.
There are good reasons to change how gifted programs operate, even putting phasing them out on the table, though the reasons in the article are ideological, which is practically the definition of what you have when you don't have experience - just the logic of an idea. NYC may do the right thing for the wrong reasons, and the benefits will be an unintentional side effect.