I will stipulate that the NYT editorial board has lectured Silicon Valley on diversity, though it is not diverse itself, and its female executive editor made less than her male predecessor: http://www.aei.org/publication/silicon-valley-gets-stern-lec... http://www.businessinsider.com/nyt-explains-female-editor-sm...
As for the rewrites, changing the lede graf to "entrenched sexist culture of Silicon Valley" is significant. It replaces neutral reportage -- "a week of ceaseless criticism" -- with the newspaper asserting as fact that Silicon Valley represents a more "entrenched sexist culture" than, say, the NYT newsroom itself. It's intended to frame the story in a typical high-level next-day NYT fashion by injecting the author's, or editor's, perspective. It's excellent journalism when it's accurate, but creates the type of controversy you see here when it's not.