It's moral dilemmas like these that make me prefer roleplaying in Piratez instead of Files. The pirates never had a clean slate, bootlegging, abduction, thralldom and of course rampant piracy are all parts of their existence, but they also fight against imperialist tyranny and for the downtrodden masses. Better a criminal than answering to a suit who believes the world citizen should resemble the average Redditor, and is paying fat stacks of cash to make it so.
Then again, perhaps you, as X-Com, are the only true defender humanity has left, and if you fail, a future of subjugation by aliens, rampant diseases, poverty, death and widespread radiation awaits. Yes, the imperialist action of Shogg was nasty. But before you pass judgment, remember this:
The human race has practiced true, full-fledged imperialism, as defined by satisfying the interests of nation-states at the expensive of the weaker, for a few thousand years at best. For the invaders from beyond the stars, this is but the blink of an eye. They have been pursuing imperialist ambitions for countless aeons, bent worlds beyond counting to their will. They have been playing this game long before the first caveman discovered fire, and Earth is their next target. Make no mistake, you have more in common with the nascent Zulu Nation than the British Empire, you do not get a nation addicted to Opium so Londoners can have their tea, you fight for the right to exist as a free people, and occasionally, that means engaging in brutal savagery because yours is the weaker hand, you are technologically inferior to your enemy and less experienced, and sometimes, the only way to compensate for this weakness is a mixture of grit, grim perseverance and a willingness to debase yourself more than the other.