Except of course, it renders Nimoy's cameo and the entire time travel aspect of the movie pointless.
Except Nimoy has already played a Spock from an alternate reality, the Mirror Universe. If he can be a Spock from one universe, why not another?
Common sense, writers' (and actor) intent, etc, etc.
Really, I could pick any episode or movie I wanted to discount from the main continuity and use the exact same argument to try and justify it.
And the time travel is just a way to say "everything you know is wrong". It's pushing a reset button while not overwriting what's gone before. (or not. For all we know the old universe was overwritten. We didn't see anything of it after Spock and Nero went through the black hole.)
Hence the movie being a reboot of Trek, albeit an in-universe one. Similarly to how the pilot episode of Terminator: The Sarah Connor Chronicles
undid Terminator 3: Rise of the Machines
"Countdown" and "The Needs of the Many" show the Prime universe (or at least some branch of it) continuing on after the events of 2387. The DTI novels detail the technicalities of how and why that can be.