Wow, this is just a very big misunderstanding on Jack's side.
First the bomb was meant for him, because he chose to stay on the island. I mean MIB was begging for him to change his mind, warning him over and over, even threating him with death. But the guy is a natural born stubborn!

My reasons,there is no way MIB could knew things could happen that way. Bomb was meant for Jack. But with a last minute event, Jack finds himself in the submarine. At that point MIB shout to Sawyer "Sawyer!", because he didn't want them to DIE! It wasn't his plan to have Jack in the submarine with the bomb. He tried to stop them but they were already gone. (Probably he thought if I can convince him to get in the submarine, I can remove the bomb.)
And when he said "to finish what I have started", he meant Widmore's people(including Widmore).I gotta love how writers can trick us again about Locke's intentions, and again.
PS. I can relate to his idea of getting from the island. And I'm not buying the whole evil thing at all. He is just a guy having hard time to convince people, like Jack!
PPS. Jack maybe right about the direct killing thing, but that doesn't change anything about Locke being evil or not. He didn't show any intention of killing off Losties those aren't obsessed with the island.
PPPS. And I have to say that by leaving Claire behind for the third time, all Losties(or who left of them) earned a death warrant in my book.
PPPPS. I don't understand how Locke can feel/see about what happened to submarine, but can't know what happened to Desmond.