Why would they have to write out the Eugenics War because it didn't happen in the real world? That's a stupid reason. Besides, who is to say that such a war won't happen? Seriously, just because it didn't happen for real doesn't mean it has to be written out of Trek lore. If anything, the Eugenics War is good for Star Trek, shows the struggle of humanity to improve itself from the devastating wars throughout its history.As I've mentioned before, the trouble with bringing back Khan is that the temporal changes from this movie don't go back far enough to explain away the Eugenics Wars.
Once the 1990s came and went w/o any Eugenics Wars, Khan was already part of the Trek Prime canon, so most of us had no trouble continuing to accept him as such. But if Abrams were to reintroduce Khan to the reboot canon, he'd have to either (a) explain to filmgoers how Khan could have come from an era that's in our past, but events that never happened, or (b) rewrite Khan so that he is effectively someone else, a product of some other Eugenics Wars that take place sometime between the year of the film's release (i.e. 2011/2012) and the year Kirk was born (2233).
Come to think of it, (b) could actually work. They could even give nuKhan a different full name to differentiate him from Khan Noonien Singh; usually they called Khan Singh just plain Khan anyway, so they could do that with nuKhan too and most people would get the idea.
I agree, the Eugenics Wars are part of the NuTrek timeline, regardless if it happened in the real world. The Botnay Bay is out there whether nuEnterprise finds it or not. Just like Vger.