Also why is Chekov in "Star Trek Into Darkness"?
Star Trek into Darkness is in another timeline refered often as the Kelvinverse due to "Kelvin" (in this case the U.S.S. Kelvin) being a recurring name reference in Bad Robot works with Kelvin being a reference to JJ Abrams grandfather of the same name...
SPOCK: You are assuming that Nero knows how events are predicted to
unfold. To the contrary, Nero's very presence has altered the flow of
history, beginning with the attack on the USS Kelvin, culminating in
the events of today, thereby creating an entire new chain of incidents
that cannot be anticipated by either party.
UHURA: An alternate reality?
SPOCK: Precisely. Whatever our lives might have been, if the time
continuum was disrupted, our destinies have changed.
The timeline was first created in 2009 Star Trek (the previous film) where in the future of the prime timeline, Ambassidor Spock fails Romulan from being destroyed by a nebula. A survivor with his crew named, Nero seeking revenge, uses "red matter" to create an articifical black hole and they and Ambassidor Spock time travel back in the time line (at different times), creating an alternate time line (possibly a branch off. Most Bad Robot shows that us time travel opperate this way and I am pretty sure Alex Kurtzman has been quoted saying the new timeline runs parallel to the prime, suggesting it is not "gone").
With that, the point (much like Fringe and possibly LOST) is that a new chain of events ensue and challanges what can change and what can stay the same looking at the alternate TOS characters. It's basically a look at identity through free will vs fate (or reciprcoity), when one has to consider a timeline being made from another...
So Chekov can be there, because the events of how the TOS characters come together are not the exact same.