1) Scott Alexander wanted more attention, and he realized that deleting his site and blaming the NYT for it would garner dramatically more attention, creating opportunities that he wanted. He recognized that he could become a martyr to a certain group, and use that for future gains.
2) Scott Alexander is an absolute moron who did not foresee the Streisand Effect that he was going to cause.
I personally do not think he is a moron. I think he is a manipulative sociopath who knew that people who agree with him on other matters would line up to create future opportunities for him if he pretended that his hand was forced.
It saddens me that so many "smart" people fall for such transparent nonsense. There was no lapse of judgment. He is just a selfish sociopath. Nothing more.