I wonder if the Nutrek novels being pulled might have something to do with at least two of them from what I remember of their summaries delt with stuff covered in Star Trek Into Darkness.
I.E. Kirk's promotion to captain and how Spock Prime's knowledge of the future and what he's saying about it.
This is just speculation (in this thread? No...

Also, I don't fault Abrams in the slightest, even if he did have that discussion with Paramount and CBS.