Okay, so there has to be some wicked twist at the end of the season, because everything's been a bit predictable. Early in the series, we've heard that Smokie was "a security system"; that he is the guardian of the temple and all that.
The crazy mom seemed to think that he was the special one, that he would be the one to take over guarding the island. Whoever she was, she was capable of mass destruction...filling in a well, slaughtering a village...all by herself!
I think MIB is the true guardian of the island, but he doesn't want to be. Crazy Mom made Jacob immortal and made him think he was the guardian. Or maybe he began to realize that he wasn't the real guardian, which is why he can be killed by just anyone. MIB can't be killed by anyone. We've already seen that.
It seemed strange that if Jacob were the guardian of the island, he would BRING PEOPLE TO IT. Maybe he figured out that he is only the de facto guardian and that MIB is the real guardian. Maybe that's why he brings people to the island; to coax MIB's true nature out.
Maybe that's the real nature of their disagreement. Not that humanity is good or bad, but which one of them is really meant to guard the island?
Yeah, there's probably holes in the theory, but I thought it might be worth considering.