This isn't a theory, just an interesting observation I had.
Both Mother and the MIB state that people come, fight, destroy, and corrupt. Yet they themselves seem to be at the root of most of the betrayal/destruction/corruption that happens on the island. The village from Across the Sea was destroyed by Mother, not by anyone else.
And much of the deaths of the show have been orchestrated by the MIB. Sure, Ben chose to betray the Dharma Initiative, but he did so because the MIB appeared to him as his mother, which would cause Ben to seek out the Hostiles, become found by Richard, and then to later betray them during the Purge. Through Ben, the MIB successfully eliminated the entire Dharma Initiative.
And what the hell, a theory about Jacob's cabin. It seems possible that the MIB cut the cabin off from Jacob for the purpose of making it so that there would be no one there for Ben to commune with, thus creating the anger that he later used as reason for killing Jacob.