I quote from the original article: "This isn’t about that specific agent; we’d gotten other rewrite requests before this one. Previous agents had also offered to take a second look if we did rewrites… including cutting the viewpoint of Yuki, the gay character."

Further, this presumably cannot be about only one publishing house, as a problem with only one publishing house would not really make a significant difference to an agent's chances of selling the story, would it?

The claim -- which I don't have the evidence to support or deny, but I think regardless we need to accept it as the thing being claimed -- is that this is a common thing and that narrowing it to only one or two agents or editors misrepresents it as a problem with specific people rather than a broad systemic problem.

I don't think that has anything to do with what I would call a "whisper campaign".