The reason for the firing was elucidated in the memo: his views on abortion (which the editorial staff was aware of before they hired him), was that of science: and that a fetus is a human life. His beliefs were of the side that killing a fetus was tantamount to murder (and that abortionists should be punished accordingly): a view far to the right of my own. That view is no more morally offensive than the other extreme that says full term abortions of viable babies is nothing but eliminating bio-waste. That latter is the view which plenty of staffers at the Atlantic hold, including Jessica Valenti, who also writes for the Washington Post, and The Guardian US, without any concerns of retribution.
For his callous and violent remarks (that abortionists should be punished), made years before the hiring, Gates claimed that Kevin Williamson needed to be let go. While the Atlantic has no problems paying the salary of Ta-Nehisi Coates, who compared a police officer who shot a Howard University student to the 9/11 terror attacks, or when contemplating income inequality between Blacks and Whites in America he opined longingly that such corrections "don’t tend to happen peacefully". And in response to riots in Ferguson he defended the violence with, “What clearly cannot be said is that violence and nonviolence are tools, and that violence—like nonviolence—sometimes works.” He sounds frighteningly identical to the same things that the Alt-Right (Richard Spencer) claims, but since it's from an alt-left view, the Atlantic doesn't want to condemn or fire, they want to ponder the intellectual nuances of the charges.
So the hypocrisy of tolerating one extreme, while being intolerant of the other, is something that Gates (editor) lost sight of. Or just never really cared about.
So what did we learn?
I learned that while the Atlantic’s founding motto was, “Of no party or clique”, that dream is long dead. We also learn that anywhere that progressives get a voice, they will ruin it for others. They have the tolerance of complete intolerance: there is no party or clique at the Atlantic, because like California, Nazi Germany, or anywhere else the progressives rule, they demand complete and utter subjugation to the will of the collective: thus they are not "of" the clique, they are the clique.