I think there is something wrong with thinking that the MIB is evil. Let's take a look at the information given so far.
Jacob is surprised that the MIB tried to kill him.
Jacob is trying to show that mankind is worth saving.
Jacob is willing to risk the entire planet trying to show the MIB that there is good in people.
Now, if the MIB was evil this would absolutely make no sense. Why would you risk the lives of everyone on the planet just to show evil it is wrong. Also, remember what Jacob told the MIB that he would never leave the island as long as he lived. If that was the case, why bother trying to show the good side of humanity. Also, would it come as a surprise that evil incarnate would try to kill you. Would you be surprised about that, I know I would not be. Finally, when Jacob said he could never leave maybe it wasn't a cruel statement as it was "you might not remember the reason we are here, but I do."
Here is what I think is happening:
MIB is actually trapped with an entity that if it left the island would kill everyone. This might have been the fault of Jacob but they both remained on the island with the MIB slowly losing his human side and Jacob feeling remorse attempts to bring it back. This leaves me with the suspicion that the end game for Jacob is both his and the MIB death and in their place 2 new candidates who will keep the island safe. One of which will need to be possessed by the creature (Thinking Desmond as a container), while the other acts as his watcher and tries to keep him from falling victim to it...but hopefully this next container will be the last. Desmond is special after all.