Do you mean the assertion that NYT made these changes in response to being reached by Facebook's PR team? (This is difficult to prove but suggested by the facts we have.)
Do you mean the assertion that the NYT regularly changes headlines in response to criticism of those being covered? (This is alleged, but I have no proof of this.)
Do you mean the assertion that Facebook contacted the Times after the article was published? (I highly doubt that this is false, and it being true suggests that the first point was true.)
In short, the opening paragraph, which the article leans on struck a nerve.
The New York Times offers powerful third parties the ability to
edit away–that is, to delete from the internet–unfavorable coverage
appearing in the paper of record’s online edition.
It’s false. The editorial process is pretty rigorous. No company has a magic “edit” button.The article goes through rounds of edits post-publish. It’s a established process and not done as-hoc.
Also, just because you work(ed) at a company it does not mean you are fully aware of everything that goes on there, so don't make blanket statements about what can or can't happen.
Employees are often some of the least informed about the inner workings of an organization, as they tend to dismiss uncomfortable findings out of hand and refuse to read about them.
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:
https://www.nytimes.com/2018/03/20/technology/alex-stamos-fa...
This was part of Facebook's PR push too?
Can you prove this?