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This is an argument against an assumption that many, including myself, have held about the final scene between Ben, Flocke and Jacob in "The Incident." In some ways, it's more of a counter-theory than a theory, so bear with me.
This theory comes from the scene in which Jacob acknowledges that FLocke found a loophole. Most of us have been assuming that the rule in question is that the MiB cannot kill Jacob directly, and the loophole he found was to have a third-party kill Jacob instead. What is odd, though, is that Jacob acknowledges that Flocke found a loophole before he had any idea why they are there. He says "Well, you found your loophole," before either Ben or Flocke say anything other than "Hello Jacob." Unless he's omniscient or has seen the future, he certainly does not know, at that point, that FLocke asked Ben to do something, that Ben will actually choose to go through with it or that the something that Flocke asked him to do is murder him. So, here's the theory. Perhaps the loophole has nothing to do with killing Jacob.
It's certainly possible that the reason he brought up the loophole so quickly before he knew about the murder plan is either sloppy writing or Jacob simply assumed that's why they were there -- the MiB was certainly very clear about his desire to kill him -- but if the Ben's choosing to be the agent of the murder was such a big component of the loophole, it seems odd that Jacob would immediately assume the result of that choice.
If using a third party to kill Jacob is not the loophole, what is it that made Jacob so quickly acknowledge that a loophole had been found? I certainly don't know the answer to that question, but we can look at what Jacob does seem to know at that point.
(a) He knows that Ben can see Flocke.
(b) He knows that Ben can see Jacob.
(c) He seems to immediately recognize FLocke as the MiB.
(d) He knows that they got Richard to bring him to his location.
(e) If there really is a rule that only the leader can visit Jacob, then (d) also implies that Jacob knew that Flocke has achieved leadership of the Others.
If one of these facts are the real reason that Jacob realizes that a loophole was found, there would be some interesting repercussions. For example, consider case (a). One way that could be explained is perhaps the MiB did not have corporeal form in that initial scene on the beach. As such, he could not kill Jacob. So, maybe the fact that Ben can see him means that he found a loophole around his lack of physical form. Jacob could clearly see that as they entered, so his statement would make sense.
Or if (b) is the reason, perhaps nobody on the island can see Jacob except Richard. The fact that Ben could now seem him might mean something Flocke did, i.e. the loophole, changed that. If so, this would also explain why Ben was never allowed to talk to Jacob directly; he would have never been able to see him.
Anyway, we could probably go through each one of those items and come up with multiple possible explanations. Again, this theory is not really an argument that one of these possibilities is the correct one. I just want to bring up the fact that it's possible that the loophole may not have anything to do with killing Jacob. In any case, I'd love to hear some more theories on those five items and why Jacob so quickly said what he did.