This is JJ we are talking about, the man that virtually killed all Star Trek Cannon in the first 15 minutes of the remade Star Trek movie.
As far as Trek canon is concerned, the prime timeline goes on existing just fine after Spock/Nero disappear into a timeline even worse than one where the Borg take over. Nothing is killed.
JJ's movies just add another timeline to the hundreds that already existed. His is just a little more fleshed out than most.