Even in the late '60s it was obvious that Trek's history wasn't our reality. References throughout the TOS' first two seasons alone establish a broader and more vigorous space program than what actually happened. And so if that was so different then there's no problem accepting the Eugenics Wars in the 1990s in Trek's "reality."I personally don't see any harm in moving the Eugenics War forward, especially since Khan did not rule a quarter of the world in 1996, and our genetic engineering, cryogenic and interplanetary spaceship technology is nonexistant in 2010.
I think it's important to Star Trek's mainstream popularity that it remain our future. A few little minor details like the launch of a random satellite or probe are one thing, but an epic world war, cryogenics, space ships and genetic supermen are quite another.
I say Trek's vision of the future, and the future's past, should be flexible and move with the present.
Keeping Trek viable, reachable and relatable is much more important than any "alternate reality" mumbo jumbo for the sake of a 2 second piece of dialog. Gene was right in the idea to keep the actual time period vague in most episodes. But as usual, he also forgot about that rule almost as soon as he made it.