Several people already have postulated that Jacob's nemesis could be the smoke monster. Assuming this, here's one theory on what the loophole is.
--Let's assume that the nemesis cannot kill Jacob himself. This would seem to be pretty obvious.
--A number of dead people have been walking and talking on the island. Some are known to be apparitions of the smoke monster, including Alex and Yemi. It's also been guessed that Christian could be Smokey. And now, assuming that the nemesis is Smokey, we can add Locke to that list.
--Somehow, Smokey needed to convince someone else to kill Jacob on his behalf. Smokey manipulated both Locke and Ben. We've seen both of them have direct contact with the unmorphed Smokey without meeting the violent death of so many others.
--So therefor, it would seem plausible that Smokey hand picked Locke and Ben as part of a master plan for a proxy to kill Jacob on Smokey's behalf.
(And I guessed it was Locke's body in the box from the moment I saw it :)
--Let's assume that the nemesis cannot kill Jacob himself. This would seem to be pretty obvious.
--A number of dead people have been walking and talking on the island. Some are known to be apparitions of the smoke monster, including Alex and Yemi. It's also been guessed that Christian could be Smokey. And now, assuming that the nemesis is Smokey, we can add Locke to that list.
--Somehow, Smokey needed to convince someone else to kill Jacob on his behalf. Smokey manipulated both Locke and Ben. We've seen both of them have direct contact with the unmorphed Smokey without meeting the violent death of so many others.
--So therefor, it would seem plausible that Smokey hand picked Locke and Ben as part of a master plan for a proxy to kill Jacob on Smokey's behalf.
(And I guessed it was Locke's body in the box from the moment I saw it :)
