Exactly. While I have generally held the NYT in high regard, the whitewashing of their coverage after being contacted by Facebook's PR team is immensely concerning.
The NYT reporters have denied that Facebook's PR had any influence, so why do you take OP at its word when there is no proof otherwise?
Furthermore, those same NYT reporters who apparently were cowed by Sandberg and Facebook PR published another article that same day in which the focus is on the disgruntled CSO:
That is an excellent point. The authors of the article you've provided are both authors on the edited article. It may be simply coincidence. In the absence of other information, I was concerned, albeit understanding `post hoc ergo propter hoc`. Taken with this, it seems that they perhaps wanted separate emphases for separate articles.
It wouldn't be coincidence because they were the reporters to have gotten this inside information from their sources. Their followup, which focuses on how Stamos got fucked over for his stance against Russian interference, is long enough that it would have had to been mostly written by the time FB is alleged to have put pressure on NYT to change the first story.