The fact that he slipped up at least once in the past doesn't mean the NYT should go and print it against his wishes, for zero journalistic value. They can of course, it's a free country, but it's a dick move.
If there's a clear, consistent, and disclosed reason for not revealing the subject's identity, that's one thing. But you're suggesting journalists, or worse subjects themselves, should decide whether their identity has journalistic value?
Furthermore, I disagree with characterizing the use of one's real name as a "slip up". It seems like pretty clear evidence that the author did not seriously care about their anonymity.
I'm not interested in sloppily applied generalities for the common case where people aren't a pseudonymously semi-famous writer. Give me some reasoning on this case.
Taken to the extreme, "identity" in your comment might as well apply to his driver's license number. The NYT could print that, causing him additional hassle for just as much of an addition to the story.