Re: new canon vs novelverse: worst case scenario
Honestly, I doubt it will ever even become an issue. The Abrams films are now safely off in their own timeline, and it's unlikely we'll see any new televised Star Trek until they're done.
And, frankly, if I were to bring Star Trek Prime Timeline back to TV -- and Leonard Nimoy said in a number of interviews promoting ST09 that he thinks the film was so big that Star Trek can never go back to TV anymore -- but, if I were to do it, I'd do another TNG-style time jump and advance us to somewhere in the mid-24th Century. Plenty of time for clever authors to reconcile the Destinyverse 2380s with whatever I introduce. Obviously that's just me, but I do think that the creative advantages of such a time jump -- that you'd be generally free to both play with the same basic toys (the Federation, the Klingons, the Romulans, etc.) but also free to establish entirely new relationships among them -- are pretty obvious. There's a reason Gene put TNG in the 2360s rather than the 2290s.
All true, but with Spock Prime actually IN the JJverse, does that mean that not much can be done with him ? There are unresolved questions such as what happens with his relationship with Saavik and do they have children ? What happens with the reunification movement ? These are things that could just conceivably be mentioned in any further appearances in the films.
Soon oh soon the light, Pass within and soothe this endless night, And wait here for you, Our reason to be here...