Jacob is Free Will in a human form and MM is Destiny. Destiny, if it was a person, would detest Free Will as it has the potential to mess up Destiny's plan. Destiny controls the environment to make sure what is suppose to happen, happens, but Free Will is always there in the human decision making process. To "kill" Free Will ensures Destiny will happen - there's nothing left to alter it. However only people can choose to kill off Free Will, Destiny cannot do it. For people to subscribe to one or the other, in entirity, requires only one to be present at any time - having both is almost a paradox. Hence - MM (Destiny) saying "do you know how much I want to kill you?" Essentially, I have had enough of Free Will and it must be ended. But again, only a human can kill Free Will (by deciding that Destiny is set and they can do nothing to change it). Free Will must allow Ben to stab him, as it was Ben's decision and Free Will means following whatever decision is made, without interference. Free Will can only remind them they have a choice - much like Jacob did when he touched each Lostie off the island. Had Jacob tried to stop Ben he would have violated his own belief in letting free will dictate action. He couldn't do that.
The numbers predict an end to humans (Destiny) yet Free Will still believes humans can be saved. That's the basis for the whole MM/Jacob story.[u]