The lead editors are responsible for maintaining ethical standards, and they represent the NYT. Adjust your impression of the NYT reputation based on this story. Also see the other comment on this article about Naomi Wu being doxxed, where the risk is deadly living under a tyrannical regime: the NYT hired the journalist responsible, who doesn't believe any mistake was made there.
It's just assumed in your comment that this should only be about the media outlet, and that we should ignore the journalist involved.
The problem with people trying to shut down others primarily comes from individuals. Often that's individuals on social media. In this case it's a journalist. These individuals can destroy other people's lives, yet they essentially face zero consequences for doing so.
And each time they succeed, like in this case, they embolden others to do it.
For twitter, you have a point. For something being paid for and published by an organization, this is driven by the organizational culture which pays them to do so.
