Khan tortured Carol Marcus's science team to obtain information; and then he killed them because he just felt like it.
But wait - he was always ready with a little narcissistic speech or a Shakespeare quote when putting a brain eating bug in your head, etc - which makes all the difference in the world, of course. He was just misunderstood - no savagery to see here, folks; move on.
Your examples only managed to show Khan could restrain himself when it was to his advantage - as would be expected from the conqueror
of half of Earth. How many millions died for Khan's delusions of grandeur in those wars, Jeyl?
BTW - You actually attribute humanistic reasons to Khan being forced to flee in order to escape the consequences of his rule at the hands of his ex-subjects/the people he failed to enslave? Really?