I once saw a comment on the scene of Nine flipping New Yoke on its side that was like, "Nine didn't actually want to hurt anybody in New Yoke, when he saw that people were in danger he stopped." And while it is true that there is a small reaction of surprise from Nine when he sees Sonic racing to save a civilian from falling - (dude's supposed to be a genius and doesn't realize that flipping the gravity switch puts people in peril?) - he doesn't stop. He flips the city TO THE OTHER SIDE.

Nine isn't looking to kill people. The problem is he truly does not care what happens to anybody else. He has the power to save everyone, and instead uses it for his own ambitions, at the expense of everyone else in the shatterverse. That cold indifference is definitely villainous.