1. The content of the article is still unknown. Scott — and from what I can tell most of the rest of the SSC chud community — made an assumption about the ill intent of the author for which there is no evidence. Again the hypocrisy here is delightful given how much of rationalist ideology relies on giving people the benefit of the doubt.
2. Scott's last name is already out there and is ridiculously easy to find. The idea that he was actually anonymous as the author of SSC is silly.
3. There's an implicit admission of guilt in the way Scott anticipates that his clients and the broader public will react negatively to his views. I wonder, what is it about Scott's views that makes him so certain the reaction will be negative? Why hasn't he allowed for the possibility that his clients and the NYT readership will react positively to the article? Couldn't it raise his profile and that of his blog in a way that is beneficial to both?
4. I recognize that this is heresy to rationalist ideology, but his identity matters in a discussion of his ideas, especially his political ideas. It's easier to assess his sincerity or credibility given the background his real identity provides. Is Scott really the Grand Wizard of the KKK in real life? Is he a saint who spends his days serving the homeless? Is he just some guy?
5. If nothing else Scott is making the tactical mistake of adding fuel to the fire. My guess is that not only will the NYT still publish, this entire kerfuffle will almost certainly now be part of the story. Traditional news media thrives on controversy and sensationalism. Scott has just made this whole thing far more interesting and already drawn more attention to himself via the New Yorker article. As of my writing this comment the Google autocomplete for "Scott Alexander" is his last name. His knee-jerk reaction to the unpublished NYT piece has already ensured the loss of anonymity. Seems kind-of irrational.