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Moral Event Horizon: The chryssalid-drop on a Hegemony world got this reaction towards XCOM from a lot of readers. It really didn't help that the planet's involvement was limited to being the selling site for the slaves taken at Mindoir and that those who actually organized and conducted the raid had been discreetly taken captive by XCOM operatives. So the strike itself basically did nothing except kill anyone there who most certainly had absolutely nothing to do with the actual raid (re: civilians and Hegemony military personnel).
Considering that it worked to effectively end organized slavery in known space, and humanity agreed immediately afterwards to ratify a treaty to consider their use a crime against sapient life, it is somewhat understandable. State-sponsored terrorism does not make one innocent. Especially when the Hegemony has been doing slavery/slave raids in blatant violation of intergalactic law for centuries. Also, the Hegemony was stupid enough to push one of humanity's biggest and most traumatic Berserk Button's. The fact is, XCOM knows it was an atrocity, but hopefully something that would ultimately save far, far more lives in the long run by making a brutally effective statement that never needs to be made again. XCOM is extremely protective of humanity, understandably, and overkill is their standard response because of the horrors inflicted on them in the past.
The most ironic part being that this is precisely the reason given by Jack Harper (canon's Illusive Man) as to why Cerberus effectively engineered the event. To paraphrase a direct quote, "...thousands have died so that billions will live."