It doesn't have a particularly obscure rationale: it's a game of chicken with the NYT to pressure them not to publish his real name. He's decreased the benefit to them by making the article an irrelevancy if they do publish it, and made it costly as an action by making lots of people upset at the NYT if they do publish it.
I think, if anything, deleting the blog only raised the stakes. It definitely increased the publicity of the blog and the interest of the general audience to read his writing, which is still readily available through Internet Archive, and NYT can link it in their article. Far from becoming an irrelevancy. Also the more drama, the more interest NYT will have to publish a piece on it. So, his explanation that no blog = no story does not convince me. This is why I think that his action had a different goal, if he was rational in it. (Well, I think, his real goal was to make it maximally public, and make his followers and bystanders to go mobbing against NYT, or something like that.)
It's unclear to me what the best course of action for him actually was, given the Streisand effect. I tend toward thinking that taking down the blog was an emotional outburst at the NYT not respecting his request, and that he could have probably gotten a good outcome, both for his community and real career, if he accepted the press and maybe tried to negotiate the use of his real name down to a single instance, e.g. Scott Alexander, born Scott Alexander Scott. But I see it more as a fit of pique than anything else, not an intentioned effort to cause an internet freakout.
I was originally quite supportive of the choice made but it really has a smell after some reflection. He seems quite open on twitter in front of 50k followers about his real name.
His twitter bio:
Scott Alexander
@slatestarcodex
54.5K Followers
I have a place where I say complicated things about philosophy and science. That place is my blog. This is where I make terrible puns.
You clearly didn't (and probably should) read his post explaining why he took the blog down. It literally says right there, that Scott Alexander is part of his name, but that the NYT would expose his _full name_ instead.
Even if he did broadcast his full name regularly on @slatestarcodex (which he doesn't), the main problem is in the other direction, as he and others have repeatedly noted. The worry is that people (i.e. patients) can go from Scott LastName to SlateStarCodex, not the other way round.
That's not his full name. IIRC Scott Alexander is just his first and middle name or something, and the journalist was going to lay out his full name for everyone to know.
