I think the Prime 2387 continues onward from the creation of the Red Matter black hole that sucks in Spock and Nero. After all, this has been variably described as an alternate reality, a parallel quantum reality and a new timeline that runs alongside the Prime one we're all familiar with but doesn't erase the original.
The 2009 film doesn't specify that the Picard/Sisko/Janeway 24th century still chugs along as normal after Spock and Nero disappear but I'm assuming based on what I've read and heard since the last film came out that the Prime timeline still exists and goes forward, with the Federation and other Alpha Quadrant powers facing the ramifications of the destruction of Romulus and the potential shift of power that would create in the already-shaky environment in the years following the carnage of the Dominion War.
That's how I understand it. It's still there, but Spock Prime is now stuck in the new timeline.