The explanation is pretty easy: ALL of the JJverse-movies take place in alternate realities. Even the part that we thought were in the "prime". This is a universe where humans built a "USS Kelvin" that is clearly much bigger and more advanced than the "prime" Enterprise later, where Khan always was a white Cumberbatch terrorist and not an asien world conquerer, where "Praxis" exploded already before the Narada arrived, and where the Federation had already built a "Yorktown" starbase for millions(!) of inhabitants,. Where human starships always had windows in the bridge instead of viewscreens, where the USS Franklin was the first starship to reach warp 4 and not the NX-project, where Romulan Mining vessels in the future are hundreds of kilometers long, where "Red matter" is a known substance, where Romulans like tattoos and have bigger nose-bones but no "forehead ridges", and where our conventional rules of physics don't apply and "a supernova" can "threaten the galaxy".
The events in Trek09 thereby only changed the future of the JJverse, not of the "prime" universe. That even explains why the JJverse and the prime verse can coexist, even though in traditional timetravel always changed the past and didn't create an alternate timeline. And Nimoy and Quinto look similar enough that you can say he morphs onto them after hundreds of years. Also, alien alternate universe biology. Pretty simple, right?
Of course that would be a retcon. But a retcon, that retcons a previous (bad) retcons away again. So a "reverse-retcon"?
Anyway, I'm much more concerned about blatant disregard of actual science, than about fictional history. Real 1996 didn't have an Augment war, and when Voyager traveled back in time to the 90s, there wasn't one. Even though it was still supposed to be the same timeline with Kirk. So there's precedent.
All it would be would simply be ignoring the JJmovies continuity wise. A feat hardly anybody would have bigger problems with it, since the real-world movies would still exist (that was the argument of the reboot fans, right?), and it would even allow the filmmakers to reboot again after tose movies have run their course.
I would simply aknowledge the cast and the style of those movies because they are popular and successfull. But continuity-wise they have already proven to be a bigger clusterf*ck than Trek ever was, which is no small feat. Simply declaring all of Trek09 as an alternate reality would actually smoothen continuity a lot and help restore some sort of logic into the Trek universe.