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.
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.