Damn, nenjin! That's some quality grim dark right there. But! If you think about it, those Frontier Worlders knew something, somewhere was going to either eat them or enslave them eventually, and by the time Black Crusade-lite capture them all they were probably resigned to their fate.
Also, had Xenos taken them as slaves directly, the Imperium would have lost good humans and an entire spire of Astropaths and gained nothing at all. Plus Xenos get free slaves.
Instead, the Rogue Trader and crew (whose sole purpose is to profit for the Imperium) both made profit and denied the Frontier World to Xenos scum. It might have been the wrong decision morally, but economically and pragmatically, it was to the benefit of everyone. Except the slaves.
Grimdark