Even before this suspension there was recent evidence that in non-advertorials The Atlantic was willing to call out Scientology. Googling "scientology site:theatlantic.com" yields, for example:

http://www.theatlantic.com/national/archive/2013/01/a-wonder... (dated Jan 14, 2013. Weirdly uncritical, simple praise for a book on Scientology)

July 2012 The Atlantic: "Psychiatry vs. Scientology":

http://www.theatlantic.com/health/archive/2012/07/scientolog...