Let me preface this by saying: I want the ALT to be the endgame. I always thought from the beginning of the season that it would be the end game. My last theory is even my statement of how I thought LOST would end: with Jack destroying the island and everybody living happily ever after in the ALT.
But the more I think about it, this just cannot be possible.
Going in to the finale, it is clear that Flocke wants the island destroyed, and Jack must protect it for "as long as he can." This leads me to believe that the ALT is, in fact, the timeline that happens when Flocke wins. Jughead goes off, our losties never crash, Flocke is able to sink the island. In the other timeline, Jughead never went off, and our losties are there to play the game.
If Flocke wins, then it appears that people get the lives they wanted. Sayid gets to see Nadia again, Jack is a father, Kate (I think) is innocent, etc. But be careful what you wish for: although Sayid got to be with Nadia again, lo and behold he still ends up killing and going to jail. Jack was a father, but divorced and still has no woman. Kate is (again, I think,) innocent, but still accused.
This leads me to further believe that the ALT simply cannot be the timeline that survives. Sure, maybe our losties are going to get together and have a moment where they remember anything, but then what? Desmond will still go to jail for attempted murder and aggravated battery. Kate and Sayid will still get scooped up by the feds eventually. This isn't the perfect world; it appears to be, but cannot be. They made a deal with the devil, and it is bound to go sour.
In the main timeline, however, Jack can still protect the island. He can still stop Flocke from sinking it. I believe this is what will happen and because of Flocke's defeat, the ALT will cease to exist. The island lives on. I do not believe this defeat will necessarily end in death, however, because I think the final scene in LOST will be Jack and Locke/Flocke on the beach. "Do you have any idea how badly I want to kill you?" "Yes." LOST.