The whole idea of Space Seed is to create a little ambiguity/mystery about who Khan is. If they just automatically assumed he was a menace, it never would have provided him with the opportunity to seize the ship. That does not mean the writers wanted the audience to sympathize with Khan. By the time he shows his true colors, he's as bad as bad can be, period. (This is also true in the plot of Into Darkness, BTW. Where Into Darkness deviates is by pumping up a home-grown problem with Admiral Marcus, which was not the case in Space Seed.)
I think it's really misguided to go on a moral-relativistic tangent about Eisenhower and Churchill. It's simply not the same. Khan shares a lot of similarities with Hitler, or maybe more accurately a Hitler youth who bought the kool-aid about genetic perfection. There is no question that the audience is meant to side against everything Khan stands for.
There are always going to be some people who side with dictators. Certainly Hitler, Pol Pot, etc... had followers who were not forced into servitude. It doesn't mean that figures like these were on equal moral footing with Churchill or Eisenhower just because, well, the allied powers committed the sin of killing lots of people to win WWII. If that had not happened, most people posting on this board would be writing in German, or more appropriately, Trek probably never would have been produced in the first place.
As a WWII vet, I'm certain Gene Roddenberry, despite his pacifism and utopianism, realized that sometimes war is necessary, and war is hell.