Spock and the Nerada both, one after the other, went into a red hole, and shat on Jim Kirk's birth.
If the Nerada changed time so much (Nix Vulcan) that a future where prime Spock and the prime Nerada are pushing with their shoulders to head into the past, then the ship second in line would have vanished as the prime timeline was over written, and could not have followed the other one into the kelvin timeline.
Just for a minute, maybe it was Spock going in second, existed in the prime time line, after Nero created the Kelvin timeline.
My guess is that the Kelvin timeline was one of those already-existing universes - like with Defiant and the Mirror, they traveled back while shifting over.
Alternatively, being within the realm of the event that is enacting the rewrite, there may have been a delay or a protection involved by being within the events gravity/EM field/something sci fi. Until the Kelvin-verse gives me a definitive ending/reset button restoring the Prime, I'm going to go with "always existing alternate."
This is all my personal choices and perspectives, of course. To each our own.
