IMO the Khan in TOS was a lot less dangerous than the Khan in nuTrek. In TOS in the byplay where the crew were teasing Spock about the great qualities of Khan, it was shown that he liked to control the 'sheep' not destroy them. In Space Seed it didn't sound like Khan was really out to destroy anything just gain power over the Earth from his 'brothers'.
I don't know what happened to this nuKhan, perhaps Marcus tortured him or perhaps it is just nuTrek making Khan 'up-to-date'. Do you think Kirk would have let Khan go in TOS if he thought Khan was out to destroy/subjugate the Earth, even in TWOK he didn't seem to have that agenda?