There's nothing Star Trek can't solve with time travel. Need a few 1980s whales in the 23rd century? Not a problem. Hop back in time, cover Spock's conspicuously pointed ears with a headband, pack some whales in some transparent aluminum, call it a day. It will work out. Don't worry about it.
In a recent interview with TrekMovie.com, Star Trek co-writer Robert Orci has revealed that the trend is not over (spoilers, I guess):
TrekMovie: From the trailer, and certainly from the four scene preview, there is no doubt that things are different. Pike and Kirk are hanging out in a bar. The ship looks different. Kirk is on the Enterprise and not headed to the Farragut. People are seeing Romulans…things are different. Now it has been revealed in the Entertainment Weekly article that Nero goes back in time and attacks the Kelvin, and JJ also talked about this during his previews. So the big question is: Is the destruction of the Kelvin, the canon reason why everything is different?
Orci: It is the reason why some things are different, but not everything is different. Not everything is inconsistent with what might have actually happened, in canon. Some of the things that seem that they are totally different, I will argue, once the film comes out, fall well within what could have been the non-time travel version of this move.
TrekMovie: So, for example, Kirk is different, because his back story has totally changed, in that his parents…and all that. But you are saying that maybe Scotty or Spock’s back story would not be affected by that change?
TrekMovie: Does the time travel explain why the Enterprise looks different and why it is being built in Riverside Iowa?
Bob: Yes, and yes.
Time travel is like hot glue. It can hold together almost anything, even disjointed canon, and you never notice because it's clear. Ignore that the clearness is often lumpy and has some stringy bits coming off. It works, OK? For all you know, our current timeline is only the result of Q allowing Picard to go back in time to change a 20th century event that would later destroy the Enterprise. You have no room to talk when you may well be the product of Star Trek time travel.
Much longer interview that involves science here.