Publishing classified information, no matter how innocuous or unharmful, is still illegal and it would be a dumb fucking thing for The Atlantic, or even a private citizen* to do.
However I'm to understand that since then a government representative has said that nothing in the conversation was classified and The Atlantic is now considering whether to publish everything.
Absolutely nothing about this story indicates that The Atlantic or any of its employees are "working for the government" or anything like that. They were just trying to not break any long-standing laws that 100% would land them in prison for a long time.
This is a great example if Occam's Razor. Is it all a conspiracy between the government and a news organization in good standing (ie not Fox News/OAN/etc)? No, somebody just didn't want to go to prison for a stupid reason, so he held back a little to play it safe.
*of course private citizens have published classified material before and they did us a great service by doing so, BUT that information was, generally, worth it