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.
For one thing, it's not an "analysis piece". The additional coverage in the later version includes new reported details. An "analysis" is what you write when you're done reporting and want to synthesize several stories you (and perhaps other outlets) wrote. That's not what happened here.
NPR's web site handles this for breaking stories by keeping the original article and adding updates to the top of the page, with time stamps as information is added, like this:
