Remember what Sawyer said a "Long Con" was? It's a con job where you get someone to do what YOU want them to do by convincing them that it was their own idea.
I think that Jacob is pulling a long con against the Man in Black. The same rules that prevented the Man in Black from killing Jacob would have worked in reverse. Jacob couldn't kill the Man in Black. By allowing himself to be killed, Jacob has set events in motion that will eventually result in the destruction of the MIB himself. Jacob will do this through a proxy for himself. This proxy will be all of the characters whom we saw Jacob touch in the "The Incident." Each of these characters reflects some facet of Jacob's own personality. He's a healer, a con, a vengeful murderer, can speak with the dead, etc. He has therefore "hand picked" our heroes for the final battle to destroy the MIB.