"Collusion" seems like overstating the case a little to me. I'd be more shocked if the opposite were true -- if the site publisher wanted to remove a comment, and Disqus, for whatever reason, wouldn't let them. Disqus isn't supposed to be making editorial decisions on their customers' sites; if someone wants to be an idiot and moderate out non-cheerleading comments, it's not Disqus' place to override that decision.
I suppose you could come up with a theory where The Atlantic talked/bribed Disqus into doing the moderation for them, but it seems much more straightforward to assume that it's the admins at The Atlantic who were filtering comments.
By they, I mean the Atlantic, not Disqus. Though, it wouldn't surprise me if they had contract moderator options available for companies who don't want to employ their own.
Yes ... I appreciated that one too. I'm sure they're monitoring HN since this place is such a bastion of scientists, so it might be disappearing shortly.