If they rebooted Clarke's universe, maybe they should.
They haven't 'rebooted' Trek though. Everything pre-Kelvin still includes historical events detailed in TOS and beyond.
I don't know why it's so hard to accept that in the fictional
Star Trek universe there was a war in the 90s.
Because it places Trek in a universe not remotely our own, meaning that the triumph of the society in that fictional universe is in no way actually connected with the evolution of the society in our own.
Basically, it takes one of the central premises of the whole franchise--that if we play nice, we can have a great world too--and undermines it. The future of Trek ought to plausibly be our future, not the future of a world where genetic engineering technology was being perfected in the early 1960s and interstellar ark ships were being built in the mid-1980s. Also--and I'm still no booster of seeing Khan in the Abramsverse--no audience wants to see an alternate 1992 that has no bearing on their own memories of 1992. Imagine Voyage Home being populated by bands of young Augments. It'd have been silly. Even sillier than the whale thing, and a lot less relevant. Heck, Kirk maybe could've avoided the dangers of time travel back to the future by putting himself, his crew, and the whales in freezeless stasis, apparently on the cusp of being developed in the 1980s inasmuch as it was an incredibly robust technology in the mid-1990s, and sailed out on a DY-100.