While the game [the new Star Trek MMO] incorporates elements of the J.J. Abrams Star Trek movie as they affect the "prime" Trek timeline, there is no reference to "nu-Kirk" and the other rebooted characters. As soon as Spock went back in time, he created a divergent timeline. The actions of the reboot characters don't affect events in the long-established Trek canon. Still, the Federation is left to deal with the aftermath of Romulus' destruction, which did happen in the prime timeline.
Multiple timelines. Boo! Boring.
To be fair to everyone involved, the game was in development long before Abrams got ahold of the franchise and decided to use time travel to reboot the franchise. So there wasn't a lot they could do.
But it would be a lot more interesting, in the long run, if all the events in the Trek universe that were revealed before the new Star Trek movie were actually wiped out by Nero and Spock's actions. All of the events of the original show, the Next Generation show, and so on, would only live on in old Spock's memory. That would be somewhat tragic, and evocative of the best Star Trek episode ever.
Instead, it's just another timeline (of perhaps infinite variations), which, to my mind, kind of takes the weight out of any story. And now fans have to keep track of terms like "the prime timeline" or "nu-Kirk." Blech.