Desmond has already killed MIB by Ray

Desmond was not trying to kill Locke when he ran him down in the alt universe, he was putting in motion the events to get alt Locke to remember his island life so that alt Locke could eventually jump his consciencenious to take over his island body which is now being used by fake Locke. That is how fake Locke will be defeated.

That is why Desmond was so at ease on the island, he already achieved his goal by running over alt Locke. He also already arranged the meetings of all the necessary losties, so they will all become aware of their island lives. His work is done in the alt universe. He is not afraid of fake Locke because he knows fake Locke can't kill him and he knows he has already killed fake Locke.

Locke will have to resume fake Locke's duties on the island because even though fake Locke turned evil his presence is necessary on the island. There always needs to be 2 opposing forces in the universe to keep the balance. Jack will take over Jacob's duties on the island by sacrificing himself for the survival of all the others. Jack and Locke will continue the free will vs. destiny dance that Jacob and fake Locke have done for hundreds or thousands of years and Locke and Jack have done since meeting on the island.

The other losties will be able to live life outside the island, whether in the alt universe or in the current timeline. Either way it doesn't matter because they will be aware of both universes.

The last scene is Locke and Jack on the beach having a very similar discussion as was had by fake Locke and Jacob.