I never believed the universe the Narada emerged into was the Prime Universe from my first viewing of '09 (nor did I believe old Spock was Spock Prime).
I know that was the intent but too many small details didn't add up.
There were always small details that didn't add up, like all the contradictions between "Space Seed" and The Wrath of Khan or between "The Host"'s Trill and DS9's Trill. So just having more such inconsistencies wasn't probative in itself.
But I agree that setting the timelines' pasts apart more overtly does provide a handy way of resolving such inconsistencies. It's certainly easier than trying to concoct explanations for every change, although concocting explanations can be fun.
It's great to hear that people (including the creators) are finally coming around to this way of seeing it.
Well, not exactly the same way -- Pegg said it was changed in both directions as a result of Nero's incursion, not that it was different to begin with. But functionally, it's a trivial distinction.
It's better for the creators to have this extended freedom, and it's given me a good breaking off point to not follow the books and comics in the rebooted universe. My 'To Read' pile was big enough already before the reboot.
For what it's worth, though, Spock Prime and Nero still came from the Prime Universe, in this new model. So any story about Spock Prime in the Kelvin Timeline is a continuation of the journey of the same Spock we've been following since 1966, just relocated to a new continuum. So it's not an entirely clean break.
If anything, I have the opposite reaction, in that this change could enable me to include more of the Kelvin tie-ins in my personal continuity than before. There were a lot of comics that I discounted as apocryphal because they required things to be different before 2233. Now that that's apparently feasible, I might reassess some of those stories.