I will start out as I always do, by thanking people who have inspired me and apologizing to those who have said this before and whose theories I am unaware of. I don’t read all the theories on here (half, at most).
There has been a lot of talk recently on the evil not being let off the island being connected to the infection, rather than just MIB. I was thinking along the same lines. I also think that MIB is infected, and has been infected now for a VERY long time.
Jacob and MIB were once close friends. I’m not sure how they got to the island, or their backstory, but upon reaching the island his friend either dies, or gets infected with the evil. Jacob is told by his predecessor (former island protector) that he must kill his friend, but can not do it. He still thinks there is good inside of his friend (similar to how Luke believed his father Darth Vader, had a little bit of good in him left as well). Jacob knows that although he doesn’t want to kill his friend, he can not let him leave the island in order to protect the world from the evil that will spread. So instead he keeps his friend around, trying to convince him that people are good deep down (and therefore so is he).
The friend might also be following an older person inhabited by the evil, but now is the “main” infected person. Being the island’s protector gives you power’s (Jacob’s healing, eternal life giving, etc.) as does being the main evil person (turning into smoke, taking on other people’s forms). The person on the island infected the longest is this main evil person.
Jacob has had a near impossible time convincing his friend, who manipulates and kills the people Jacob brings to try and convince him of the good. So Richard shows up, and convinces Jacob to be a bit more hands on. Everything in the show stems from this.
Jacob feels a bit guilty about his friend, and is willing to die to try and make his friend see the good, or maybe even drive the evil from him. This is why Jacob is never angry at MIB, even when he wants to kill him (and does). He is a friend and Jacob feels partly responsible for his situation.
In the end I believe the evil will be released from Flocke, but not from the island, as Sayid becomes the new main evil guy (I think Claire will die soon) and probably Jack becomes the new Jacob. But I’m not sure about Jack.