He said that about MIB getting off the Island. We've seen that in the FS reality, neither of them have stopped existing. Ji Yeon and Charlie Hume haven't been born yet, but neither were they in the prime universe in September/October 2004. And Desmond has evidently flashed to the FS reality and back, which means that they can co-exist, and the world did not end.Terrific episode, but I dunno if it's smart for the writers to want us to believe the sideways verse is the "wrong" one. As a threat that needs to be avoided, it lacks punch. Several of the characters (Ben especially) have better lives in the sideways verse and other characters are at least alive and sane. The universe seems to want to return to a state where everyone is less happy. Hmm, that would explain a lot about things.
There are clues that suggest that it's one universe or the other and they can't both co-exist. Widmore said something about everyone vanishing in the last episode.Even if the prime universe were superior to the FS universe (why? they're both equally real apparently), the existence of the FS universe is not endangering the prime universe in any way, as far as we know. Why would Desmond need to do anything on the Island?