“We screwed up.” That’s what The Atlantic said after it posted an online advertorial from the Church of Scientology, provoking a Twitter backlash and eventually leading the publication to take the feature offline.

In an interview this afternoon, a senior Atlantic official circled again and again to matters of procedure and policy. Asked just what mistake the Atlantic was apologizing for, the official responded, “It’s a general apology for not having thought this through overall. I wouldn’t want to assign the apology to a specific portion of this.”

Perhaps that’s because The Atlantic feels chastened for all aspects of the controversy. As the publication reviews the “native ads” on TheAtlantic.com, its leadership will focus on “what advertisers we’re comfortable having on the site” as well as “how to treat comments on sponsored posts,” according to the official.

Better execution on the comments alone may well have tamed the online reaction to the story. A spokeswoman for the Atlantic told the Erik Wemple Blog this morning that the magazine’s marketing people were messing with the comments. “They had to have known it was going to create some sort of a reaction, but what really made it so much worse was the way they were controlling comments,” says Tony Ortega, a former top editor of the Village Voice and an expert on Scientology.

Advertorial clients of The Atlantic had previously opted not to have comments at all on their posts, said the spokeswoman for The Atlantic. Not a bad strategy for an advertiser, given that the Internet responds brutally to propaganda, filling all available spaces to add balance and contrariness. Bet on this: The Atlantic will get out of the business of moderating comments on advertorials in the future.

The Atlantic official expressed no regret at having taken down the Scientology feature. At the same time, the official cautioned against reading too much into the move: “We’re not passing judgment in the moment on the Church of Scientology and their advertising initiative,” said the official. “I just think we’re actually trying to be really honest about the situation and recognize we’re in a little bit of uncharted waters with this ad format. Combine this ad format with an advertiser like this, and it puts you further in uncharted waters.”