I said this in another post, but I think we're close to getting one BIG answer to the questions "who wins the war between Jacob and MIB?" and "what are the flashsideways"?
In the flashsideways, the island is buried underground, but the world still goes on, negating the importance Jacob has put on protecting the island. So we know that Jacob is wrong. The world may not be better without the island, but it's obviously not worse. Now, how can the flashsideways world be connected to the big war? Simple. What we see in the alternate time is what happens if MIB wins. The island is gone, Jacob isn't there to influence the Others' lives anymore, Sayid gets what he is promised (Nadia alive) and so on. It is a remodelled world without Jacob, and guess what, it's not a disaster!
Now you ask me how did MIB manage to sink the island and negate all the on-island Lostie experience? Well, he may have used the donkey wheel, or even the numbers in a way, who knows? But the point is, he is not evil, just a man who wants to go home.