They are allowed to run ads, but media should allow ads based on ethical decisions - lots of countries treat Scientology as a criminal organization (Germany: "It views it as an abusive business masquerading as a religion and believes that it pursues political goals that conflict with the values enshrined in the German constitution" Source [1], another example from Belgium: [2] )
Running a sponsored article for Scientology is, to me, akin to running an article about the great employment opportunities at Mexico's Zetas.
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.
In newspapers and magazines, sponsored content is very clearly labeled (which arguably this is) and made to look _different_. For example, most magazines require advertorial to be in a different typeface and font size, so that readers have a sense that it's somehow "different." The difficulty here is that, unlike a magazine in which you're flipping pages, you probably only saw _this_ page and thus have no sense about whether it "looks different."
There is a Streisand effect-like phenomenon when notorious publicity-seekers become famous due to widespread criticism. The attention, negative or not, is exactly what they want. The biggest example is probably the Westboro Baptist Church.
There are "stories" to the right that are really pro-Scientology ads, but not marked as "advertisement". The whole thing feels slimy, not even considering the subject.
I have seen "sponsored pages" in newspapers for many years about a lot of crap, is there a reason to consider this one worse than the average?
(Yes, scientology is evil but they are not forbidden from making ads I reckon?)
edit: the "sponsored" bit is right on top of the page, as it is in dead-tree-form newspapers too.