It's pretty disgusting to defend bloody dictatorships by appealing to the fact that these dictatorships were democratically governed. Eisenhower Jugend had no more choice on the issue of dying for the flag than Hitler Jugend did...
If type of government really matters, let it not be forgotten that Khan was never established as a dictator (only that he fought those). All we learned of his form of government was that he was a tyrant; whatever the correlation between the terms in the 23rd century, we don't know.
That does not mean the writers wanted the audience to sympathize with Khan.
Why should we care about what the writers wanted? Trek was written when the zeitgeist was sexist, racist and authoritarian, and it shows. Luckily, it doesn't show so strongly that we couldn't ignore it and enjoy the cool bits.
In any case, in the final act, our heroes and Khan part ways in amicable terms. Were the writers somehow being coerced to writing Khan in explicitly sympathetic terms there or what?