The thing is, Khan would be a sympathetic character if he were at all reform-minded. He's not. He's willing to take personal advantage of the chaos Marcus wants to create.
And Khan freely admitted that if he were allowed to run free, he and the rest of his gang would have continued the work they were originally doing - which involved the genocide of anyone who wasn't an Augment like them. You don't get much more evil than that.
Just because Marcus was the reason Khan did what he did
in the film, or the fact that Khan cooperated - mostly - with Kirk in taking Marcus down, does not make Khan any less evil.
Khan never admits to genocide in STID - he says 'work', Spock says 'genocide', Khan gets impatient and changes the subject.
In Space Seed, that goal was the vague and 'has-the-potential-to-snowball-into-something-terrible' '
bringing the world order', and he alludes to that during the cell scene is STID with a less ominous choice of words. A goal that could lead to genocide, but was mostly used to show he had tyrannical designs.
I'd say they did that on purpose in case they wanted to bring Khan back in a less villainous role, they have an easy 'out' to say Spock was wrong. Considering Orci's a Trekkie who evidently did listen to some Trekkie complaints based on what's in th movie, it also gives him an easy avoid for the 'but Space Seed said...' complaints.
'Genocide' doesn't necassarily involve the augments going around slaughtering anyone who's not like them. If Khan was enforcing a Eugenics program whilst he was in charge, even in a non-violent way (for eg. Whacking whoever broke the rules with huge fines), then we'd say he was committing genocide.
The comic Orci was involved in also suggests he got that reputation thanks to the motivations of other Augments and his own callousness to collateral damage during conflict, rather than any actual genocial goals (for eg. Nuking Washington and Moscow to stop the Cold War and seize power.)
Which is still horrible and requires a bit more suffering than what happened in STID to redeem him, but it does better fit with what was described in Space Seed ('We wanted to bring order' 'Peace and prosperity, but at the cost of personal freedoms').
Though I'd still put Marcus as the 'big bad' of the film, simply because his actions ultimately drove everything. He was the one attempting genocide on screen, he can't claim to be manipulated like Dougherty in INS, nor is there any evidence in the movie that his paranoia about the Klingons has any legitimate basis.
Yes, indeed! 
