I've just got a thought reading some previous thories and comments.
I wonder if on the island ever been more than one "group of others". One Jacob's and one MiB's. It made me think because we saw an egyptian door with hieroglyphics telling: "To summon protection" - and it was smokie as we know it. So, maybe long before 1954 there were two groups of people fighting each other for the control over the island. Jacob's group won and now MiB wants to take a revenge by showing him "I'm quit from this game and I'm leaving". He's tired of playing this game ("It always ends the same. They fight, corrupt(...)". And maybe those groups were pretended to guard the two energies (Orchid and Swan) [capture the flag? :D]
Any other pros and cons are welcome.