Marcus acknowledges he took a 'tactical risk' in awakening Khan because he wanted his specific abilities to respond to, as Khan put it 'an uncivilised threat in a civilised time' but I can't actually recall what 'Space Seed' said about his rule.
In one sense a tyrant is a tyrant and he was excised for a reason. I would have to go back to the episode again. Khan in TWOK (or in fact STID) may not be the most reliable source of information about himself given he already managed to blame Kirk for his own fate. And he was quite blatantly murderously intentioned in 'Space Seed' itself.
That said, the term Eugenics Wars seems to indicate some issues.
'If the Apocalypse starts, beep me!' - Buffy Summers
'The sky's the limit.....' Jean-Luc Picard, 'All Good Things'
courtesy of Saquist