I believe Jacob and the MiB are old friends. Jacob cares about MiB and it trying to save his soul. The only way he can save MiB's soul is to have him admit his sins and repent. Jacob cares so much for MiB that he was willing to sacrifice his own life to save him. We now know Jacob can really handle himself and could easily have killed Ben when Ben came at his with the knife. (On another note I think Jacob's plan also involves saving Ben).
Jacob mentioned something about proving MiB wrong as if is the only thing he truly cares about. Why is that so important to him unless MiB is important to him.
Could it be the entire 'game" is to finally prove to MiB that people are not all evil and he should be sorry for that he is is done wrong. In the last episode (Richard's Episode) Richard asked Jacob to resolve his sins, but Jacob is unable. Therefore Jacob does not think he is a god. Perhaps only Richard can resolve himself of his own sins.
From what I heard last night Jacob is the one that took away MiB's body. He did not kill him so either is is unable or wanted him alive. My hunch is that MiB can not be killed by another He must kill himself. He will only kill himself, however, when he feels remorse from his actions. Thus it (MiB's life) only ends once.