They can't destroy if they don't come by Lost Baby Boomer

I believe that Jacob is from one reality (be it alternate timeline or parallel universe) and MIB from another. The island is somehow between the two worlds and there will be a war that decides which world will win.

Jacob is in the world that we have witnessed in Season 1 through 5 and MIB is in the one we will see in much of Season 6.

Jacob keeps bringing people to the island to the dismay of MIB. As MIB stated,” they come they fight and they destroy." (Looks like he is right about that, people do keep “blowing things up”, even the Black Rock had dynamite.)

Jacob brought the Losties and MIB would like to send them back or make it so they never came at all. (Jacob may have brought the Egyptians, the US Army and the Dharma Imitative and MIB may have worked to get rid of them too.)

In the case of our Losties, Jacks’ explosion plan may have allowed MIB to push the Losties into the alternate world, as if the plane crash never happened at all. This would serve MIB’s plan. They can’t destroy if they don’t come.

It does look like MIB may have been foiled again though, because the last thing Jacob says is “They’re coming”.