The reason for the loophole was to make sure that the two armies that are about to go to war each have a leader, and what better military strategy to confuse each side than to have each leader look exactly alike. This ensures a far fight because both sides have the advantage of manipulating the other into thinking their leader is the correct one. So MIB & Jacob found the ultimate patsy, John Locke, a man who needed to believe, so they both manipulated him into worshipping the island, they made sure he would die and they manipulated Ben into "killing" Jacob. Jacob & the MIB cannot die and soon after Jacob "died" his energy went into the corpse of John Locke on the beach. So in Season 6 there will be two John Lockes, one inhabited by Jacob, the other MIB in disguise. Both will be the leaders of their respective armies in the war on the island. The war is the final way for Jacob to prove MIB wrong, that it only ends once and anything before that is just progress.
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