Earlier quoted context omitted.
"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.
""Collusion" seems like overstating the case a little to me." Aren't they editing the comments for their customer?
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.