Three issues come to mind.
Issue 1: I wonder if the reason for their being on Earth (and other places) is understandable...but we can't for the same reason it would be difficult to explain the Lunar Landings to the people who personally built Stonehenge.
Issue 2: Oh please don't do this! Don't turn into another of those "emotionless aliens vs sentimental and emotional humans."
Since you have aliens, let them be alien!
ie, let their fear at the uncontrolability of the rebels, be for the same reason a cod can't understand human laws about infanticide -- biology.
Issue 3: Though the alien was right -- if they had wanted to commit genocide, they would have, and there would be no humans left.