Maybe it is the optimist in me that refuses to believe that Jacob is evil. People think he has been controlling everything, but he said to Ben that he "has a choice. We all have a choice" [sic] The whole story raises some interesting questions about faith and scientific reasoning.
At the beginning of Season 2 Locke asked Jack if he was a Man of Science or a Man of Faith. Jack, at the time, was leaning toward science, only believing what he could see, but ignoring the miracles that he had already seen happen, such as his wife walking again, and his dead father wandering around the island. Locke, on the other hand, embraced faith, even though in Season 4 (I think) when we learned about Locke's life, his high school teacher told him that he excelled in science. For some reason, Locke adamantly denied this about himself.
Ultimately, both characters made a series of mistake after mistake, one only believing what he could see and the other going by blind faith. Somewhere in between lies the foresight to make the right decisions, and this requires science and faith. Jack has been through hell to get to that point, so I cannot believe that yet again he is making the wrong decision.
As for the people following the MIB right now, (Sayid, Sawyer, Kate and deceased Locke, for that matter) I think they will be redeemed and/or saved by their alternate selves in the alternate reality.
YEAH RIGHT!!!! 
