Journalists obviously never tell their subject their piece is going to be negative. In fact, as far as I can tell from the few people I know who have been in that situation, they appear to routinely say the opposite.
...and who would know if they'd just used his pseudonym?
It's not like a large % of the NYT readers are going to know straight away that no one exists with the name used in the article deviate from it at all?
In the News, to normal people reading an article, it's more interesting to hear about about a real person with a real life, with a real family, home etc than a pseudonym with no background. It sucks but that is how the News usually works, and how people like reading stories about other humans. Hopefully in this case they might see the damage that this might do.
I'm pretty sure Scott would have been more keen to share details about his personal life if his pseudonymity had been guaranteed; I know I personally would have in his stead.