The prime Star Trek timeline still exists. It is well established that alternate timelines can branch off of a prime reality without destroying the original. This is proven in both in "Mirror Mirror" (TOS) and "In a Mirror Darkly (parts one and 2)" (ENT). The alternate timeline in which the Terran Empire exists in place of the Federation split from the prime reality in 2063 when Zefram Cochrane killed the first Vulcan that officially made contact with humans. This is obviously completely different than what happened in the prime reality. This split in time shows that alternate events can lead to alternate timelines, but that does not mean that this split in time destroys the prime timeline. There are other instances of course, where the original timeline is destroyed [EX:"Year of Hell" (VOY)], but the timeline in which Star Trek (2009) occurs does NOT destroy the original timeline. From the real world perspective: do you really think that JJ Abrahms would have made his movie establish that all other events in the prime reality never occur? I agree that occasionally, Abrahms does not hold true to the true Star Trek principles, but not even he would do something as sacrilegious as destroy the original timeline of Star Trek.
And if that doesn't prove the fact that the prime reality still exists, please be reassured by this, which is taken from Memory Alpha (the Star Trek wiki): The writers of Star Trek, Alex Kurtzman and Roberto Orci, were asked about the implications of the new alternate reality that was introduced in the film in an interview. They explained the new reality runs parallel to the prime reality as a new quantum reality, as the concept was explained by Data in the episode TNG: "Parallels".
