There are actually differences in the Prime and Kelvin timelines that happened before Nero's incursion. For instance, Kirk's date of birth is off by several months. They tried to justify that afterwards by saying something about the event sending shockwaves through time to change things before it even happened or something like that. The real reason probably lies in that interview where JJ Abrams admitted he never liked Star Trek, but you could argue that the removal of various down-stream time travel events, like the events of "The City on the Edge of Forever" likely not happening in the modified timeline, could actually cause retroactive changes to the timeline.

But anyway, the Kelvin timeline already diverges before the Kelvin-Narada thing, because reasons.