Sure, and you'll notice that I didn't say there's no problem at the NYT, or that the organisation as a whole should be exempt from the actions of some set of it's staff.

I'm just saying that the analogy to an (offensive) action by a specific person, toward a specific person, is a poor analogy for the actions of some subset of a large organisation, which almost certainly isn't directed at a specific person.

And I doubt many people would equate the actions of the NYT with literally being spat on.

He is right to blame the org and “paint them with the same brush” as errant employee if they do not own up to their mistakes; especially if it concerns something that is part of their main product. Can you imagine some tech company having a data breach because an employee was careless and NOT admitting to the breach? People lose their jobs for that kind of mistakes, not get a pat on back.