I'm still loving the 'prime' timeline in the novelverse - it's dynamic, changing and very well done. It is and always will be my first love.
I'm also enjoying the new continuity, but not quite as wholeheartedly as the older one.
I can't see the new continuity being canned, but in its present form it has a limited shelf-life. Movie contracts and film star cast members won't give the sort of longevity you get with TV shows. At some point Pine, Quinto and co. will move on and necessitate another reboot, a spin off or a jump forward in time.
I wouldn't be hugely surprised if a show or film set in the 25th century or beyond doesn't happen, working as a follow-up to either timeline. Most of the differences in takes on the TOS era wouldn't be noticeable after a couple of hundred years, although the loss of Vulcan and/or Romulus may need some inventive retconning...