MIB is not able to kill Jacob.
But a mortal can. Who would want to kill Jacob from the Others?
Only one who feels jealousy towards another who gets Jacob's unmerited favor, and then in turn resents Jacob because of it.
But no one can get close enough to Jacob unless they are a leader.
One wouldn't be enough: Ben on his own without any object to resent or feel jealous of wouldn't have been pushed far enough to one day say "you know what, I think I'll kill Jacob". He needed that extra push.
Two must be selected: the patsy, and the pawn.
Locke and Ben were hand picked. Desmond could've been picked as well to crash 815 to get Locke to the island.
Events had to play out so that Ben would move the island and Locke would leave the island and die. This would enable time travel that would help confirm to Richard that Locke was "special". It would also necessitate Locke leaving to prevent his friends on the island from dying as a result of the time-jumping. As you may have noticed, the time travel stopped not as a result of Locke leaving the island or coming back.
Ben was nurtured and tricked by the MIB, not Jacob. Ben received orders from Jacob via Richard, but did Ben take Locke to the 4-toed statue to meet Jacob? No, he took him to the cabin, where MIB was trapped by the ash. Ben went to the wrong place. Someone, whether Hurley or Locke, broke the ash circle and freed MIB.
Christian Shepard was really MIB who gave Locke direction to fulfill the rest of the "long con". fake-Christian told Locke to move the island (thus to get the time travel going to necessitate: a) Locke leaving the island & b) validate Locke as being special to Richard. Christian Shepard also told Locke he had to die (so then MIB could take his body, retain leadership of the Others, and complete his long-con with Ben and off Jacob).
MIB posed as Walt to try to ensure the freighter people wouldn't get to the island and mess up his long-con (If the freighter people got to the island and got Ben, thus eliminating the need to move the island/time travel/Locke confirmed as special/Locke leaving the island to save his on-island friends from time travel side effects/Locke dying to provide the host-body trickey to get close enough to Jacob as leader of the Others)
MIB posed as Alex to ensure Ben would do anything Locke told him to do. MIB can pose as anyone who has died on the island or came already-dead to the island.
Even when Ben was about to kill Jacob and right after, he seemed surprised and shocked that he had done that. It was within him, but MIB posing as Locke had to egg it on a bit. It's very possible Ben could have not done it, as Jacob said. "You have a choice".
I suppose Hawking and/or Widmore received some instruction from MIB.
"You have no idea what I've gone through to be here". Well, yeah, we do, a little.