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Going back to the beach scene in the opening of The Incident, maybe Jacob keeps bringing people until he finds one that can unite everybody on the Island and bring about peace, and the MiB doesn't think it's possible.
The list of candidates on the cave wall has an enormous amount of names, and likely all have been to the Island, and only few have survived long enough to leave, meaning Jacob has brought hundreds of people to die stranded on the Island. Maybe MiB wants Jacob to stop bringing people because deep down he actually cares for humanity, while Jacob does not, so MiB is willing to kill a few for the greater good, so that he can stop Jacob from causing lots of more deaths. MiB eventually realized that while Jacob was still alive, more and more people would be brought to the Island, so he sacrificed one life to save hundreds more.
Thusly, MiB would be the "good guy", while Jacob would not.
It would make for a very interesting twist at the least. What does everyone think?