There is much discussion about who is actually the good guy - MIB or Jacob. I find it hard to believe that either one is "good". Jacob's people, the Others, have done awful things, have worshiped him without knowing why, and he has spied on people and consciously walked into their lives, disrupting the natural course of events, to bring them to the island for his own purpose. MIB is manipulating people and has killed, and enough people seem to believe he is evil incarnate at this point that it's hard to believe he is "good", in the true sense of the word. It very well could be that he has just gone crazy because he broke from Jacob at some point.
Ultimately, it seems silly to take sides in this war. I don't know Jacob's purpose, but I know in sideways world the island is underwater and that Ben is living life as a good man, and things in general seem to be going better for most characters. I also see that the world hasn't come to an end with the island theoretically destroyed - so how important is the island really? I think it was pretty clear in tonight's episode that it isn't underwater because of Jughead - based on Ben's conversation with his dad, the Losties probably were never there in his sideways past and none of what we saw last season in the 70's took place. So this is not a reset either. This is people being free to live their lives without the island.
I think the end goal of this is that Jack (or someone else, but he seems the most likely candidate) is going to put an end to this ongoing duel. There will be no Jacob replacement, there will be no MIB replacement. Yes Jack seems to have become a wild-eyed man of faith, and somehow we should believe that means he sides with Jacob. But are we supposed to believe he has given up on reason altogether? I think we are debating who the good guy (Jacob v. MIB) is precisely because there is no good guy. I think Alt is showing us the damage caused to these people's lives by the very actions taking place on the island.
Many a war was fought over faith and religion, and still is, and are we better off for it? Or should people be free to exercise their own faith? I think this could be the root of what is playing out. The island is representing a battle fought in the name of faith, and it needs to come to an end.