Well, I think his mother simply didn't want him to leave the island because she had given him some "power" (the power of immortality) that shouldn't be let out in the real world. Also, I think she still wanted him to be the one to protect the island.
Yeah, the thing about the donkey wheel was pretty silly, but I kind of think they wrote themselves into a corner with that one. How could they really rationally explain how that works??
I don't have a problem with her torching the villagers and burying the cave - after all, she seems to have the power to create storms to bring people to the island, just like Jacob now has. She gave Jacob her powers, remember.
When this show abandons subtext, the answers seem spoon-fed and forced. See "the whispers" for an example. I'm glad they're letting us figure things out. For the most part, I think they explained what they needed to in this episode - the motivations of Jacob and the Man in Black, and the fact that there's a great metaphysical source of "power" on the island that can do crazy things like grant immortality and turn people's souls into smoke monsters.