When you run sponsored content, you're tying your brand to the brand of the advertiser who you are promoting. This usually isn't a problem, since most outfits will choose to run advertising deals with well-respected brands, and both brands become stronger (and wealthier) because of the association.

In this case, I can't imagine any outcome except for significant brand damage to The Atlantic. They had better have been cut an absolutely toe-curlingly-large check, because I expect they're going to pay for this in credibility loss pretty heavily.