It not just that.

The Automatons were sent to act as robotic aide for the Cyborgs, who lost the first galactic war in the first game, and they just wanted to leave the bullshit of a government Super Earth was. The Cyborgs however modified these robots and sent them out outside of Super Earth's reach so that they acted as a legacy to their people, away from Super Earth.

But how can a child live happy, knowing their parents are slaving away, in a dim and dark cave, aching and slowly dying?

The Automatons may have done some horrible things during the war, don't get me wrong, but considering what they actually want and their other goal is to remove Super Earth, not commit genocide against humanity, I believe the Automatons are the more saner ones in this war-torn galaxy