Can you really be both a public figure and keep your identity hidden by way of asking? There’s a playbook for this. Look at Banksy for example. If you don’t want your identity out there it’s your job to protect it. Not the New York Times.
It seems that his major issue was his full name becoming NYT-level famous, which is reasonable. I think that happens to lots of private citizens who get covered by mainstream news, like a IRL "hug of death".
If my premises are correct, then it doesn't seem like NYT's responsibility to keep his name private when he himself didn't do it.