So the saying goes, "If you meet the buddha in the road kill him". Thus, John is going to kill Jacob, but Jacob doesn't truly exist; at least as others have him made out to be. The buddha is not something outside you. It is not a savior, leader or anything like this. The buddha is your true nature that lies within each and everyone of us. The problem is, it is far too easy to worship others than to awaken to our own true selves. People on the island have come to worship this false idol, named Jacob. He has become their buddha and John is taking them there to show them that he does not exist. Their salvation lies within. John is delivering the people out of the wilderness. Without Jacob hovering over them, the others can awaken and bear witness to all the gifts the island offers to them as it has offered John, which is an enlightened life.