As someone who frequently rewrites, revises, and deletes their online comments, to me the article's changes just look like part of the writing process in a world of realtime publishing. The New York Times did not have a front page story ready within minutes of the news breaking, and unlike CNN, they didn't publish random tweets about the event as news: there's better and worse. Maybe newspapers need git repositories.…
But why not add the new story as a separate analysis piece, as the NYT often does? What did they gain by changing the original?
To me, it appears that the primary complaints in the linked article are based more on the editorial direction of the changes wrought by additional detail than anything else. There's a reasonable position that not placing the initially reported facts into the larger context and treating it as the local police blotter would be poor journalism. Thus a reasonable explanation is that the first draft did not meet The New York Times's editorial standards. This would not be surprising given the constraints of real time publishing and in light of the fact that The New York Times revises the resources at its primary URI regularly. As we expect.
We're not outraged when other companies change content at a particular URI based on their belief that the changes are an improvement. If there's a SPOT, it is the print edition not the web.