Actually, MIB could've killed Jack when he knocked him out. But he left him and tried to leave, and it wasn't until Jack tracked him down and MIB knew he wasn't going to get to leave without a fight that the knife came out.
Exactly, MIB had nothing to gain by killing Jack at this point nor did he really want to, he just wanted to get off the Island. The only reason MIB was fighting with Jack was because Jack bought into Jacob's thing about not letting MIB leave, and this originally came from his fake mother before MIB became smokie.
MIB's motivation was never to kill people for the hell of it, he didn't even want more people to get trapped on the Island like him. Remember the scene when Jacob & MIB was sitting on a beach watching the Black Rock sail in...Jacob brought the Black Rock to the island simply to prove MIB's wrong. How many people on that ship died as a result of this just to be used to prove MIB wrong? MIB didn't seem to want them on the Island, I suspect because he doesn't want more people trapped on the island like himself. MIB was definitely smokie by this point, and wanted to kill Jacob...so wouldn't he welcome the Black Rock people he could use to kill Jacob for him & possibly help him get off the island? Nope, seems like MIB was pissed at Jacob bringing people to the Island and then decided to use this opportunity to try to get Richard to kill Jacob. Now thinking about it, I think MIB only killed the officers on the ship when they started killing the prisoners. Then after days watching Richard suffer couldn't take it any more and saved him. Of course he'd be pissed that Jacob caused all this, so concocted the plan of getting Richard to kill Jacob for him.
And how many others were brought to the Island and died because Jacob wanted to prove MIB wrong and/or to be a replacement to Jacob? If Jacob needed a replacement, why not promote Richard?! But nope, got to bring down flight 815 and kill a bunch innocent non-candidate people in the process and then eventually as a result. Oh no the candidates got off the island....lets bring them back on the Ajira plane with some more red shirts that will eventually all die. And dead is dead, they died on the Island which is supposed to be "real life", we see a bunch of them in the side universe again....but that doesn't make everything okay as side universe IS death. Just because there's an afterlife now doesn't make getting people killed okay.
The more I think about this, the more I see Jacob as the real "Bad Guy" here. He brings people to the Island just to prove a point to MIB, and as a candidate to replace himself...regardless if other people get killed as a result. Both are unnecessary as proving MIB is wrong results in nothing and Jacob can replace himself with Richard or an Other (Also why doesn't Jacob just get Richard to bring his candidates to the Island via the sub like Others recruits thereby avoiding the unnecessary red shirt deaths?!?). So Jacob's job is to protect the Island from men who might meddle with the cork thereby extinguishing the light. Well, it doesn't seem like Jacob's doing a good job of protecting when he unnecessarily brings unintentional people to the Island (Red Shirts) and lets them wander around. Doesn't this increase the risk of somebody uncorking the island by accident?! If you add up all the people who died indirectly by Jacob's unnecessary actions, and all who the MIB killed directly to get off the island....doesn't Jacob win the kill count?
When Jack replaced the cork and the light returned, the world was once more safe. However, if Locke was not killed before the cork was replaced, then Smokey's power would have been returned to him and the danger/battle would resume (and no 'end').
So taking the cork off makes the light go out everywhere, which the fake mother says to MIB & Jacob that it's bad. Short term, this doesn't seem to affect anything other than wrecking the island and removing the smokie power from the MIB. We see that putting the cork back on restores the light and other than that, apparently no lasting ill effects. The only person that can take the cork off is Desmond because he's immune to the effects of electromagnetism. Jacob supposedly gets Whitmore to bring Desmond to the Island as a failsafe against the MIB (Presumably to make MIB lose his smokie powers so he can be stopped from leaving the Island). MIB originally wants to kill Desmond not knowing what he's up to. So it seems like MIB's goal is not to put the light out. Later MIB finds out what's the deal with Desmond, and only then he decides he wants to destroy the Island so he can get off the Island and not because he wants to put the light out. But MIB knows supposedly if the light gets turned off, it will turn it off everywhere. If that's bad, then even if MIB got off the Island wouldn't that be bad for him too? I think this could only mean either MIB expects somebody to put the cork back on after he escapes but before something bad permanently happens, or nothing really that bad actually happens. I doubt MIB would want to leave the Island only to have either the world destroyed or all humanity killed. If either of that happened, what's the point of MIB leaving because either there's nowhere left to goto or he can't be with "his" people as they're all dead.
It seems to me that it's only Jacob that doesn't want the MIB to leave. Not because MIB will make the world worse, but because his mother didn't want him to leave and/or Jacob doesn't want MIB to leave too. Additionally Jacob would risk taking the cork off (which is really bad in his and fake mother's opinion) all to stop MIB leaving. That sounds really reckless of Jacob if his job is to protect the Island and to ensure the light doesn't go out. I don't remember preventing MIB from leaving part of his job description as Island Guardian, it was more something his fake mother wanted.
Whoa, I really went off on a rant here, LOL. I guess I'm just upset none of this was touch upon in the Finale.
Summary: Jacob bad, MIB not so bad.