I'm thinking that maybe Jacob has ressurected in the form of Sayid. Jacob DID send the letter that said if Sayid died than they would all be in big trouble. But maybe Jacob was actually planning on him dying (since they actually drowned him because they had to wait until the hourglass ran out) so he could come back as Sayid. Jacob gave Hurley that guitar case with the letter in it because he knew that this was going to happen and that's why he didn't fight back when Ben was stabbing him to death. He knew that he could ressurect as Sayid once he died.