Khan was ruthless, but also practical. I think there's a big difference between being in a survival situation with a very specific set of goals versus being in a position of having power over large swaths of territory. Before resorting to trying to gas everyone, he tried to charm and beguile. He only became violent when it became clear it was the least risky way to his goal. He enjoyed being manipulative, and he enjoyed being admired. If he could achieve both of those goals without violence, I think it would have fed his ego a great deal more than having to quell uprisings or make ham-fisted power plays against people he viewed as inferior.
I didn't see that in his characterization at all. He wasn't a psychopath just for the sake of murdering. He saw the people around him as tools for his use. If you murder everyone, who is going to grow the food, make your clothes, keep the power on, etc? Ruthless, yes, and vindictive when crossed. Out of control killer just for the sake of it? We never saw that.