I'm not sure why we even have this in spoilers, so if you don't want to read anything about Jacob, the MiB, their mother, the Smoke Monster or the DVD commentary of the episode
Across the Sea, skip this post.
Anywho, I'm not a proponent of the theory that their mother was the Smoke Monster (or in this case,
a smoke monster) regardless of what I posted above about the commentary on the DVDs.
That being said, I don't think the theory undermines anything we've seen in the show. It's my belief that the Smoke Monster is just a pure force of nature. It has no goals, no evil plans, it just wants to exist and survive. The problem with that is that by existing it threatens the lives of everybody else. If you're a comic book geek, think Galactus. He could be described as "evil" by those he threatens, but in reality he's just doing what comes naturally to him.
The motivations of the Smoke Monster we saw through 6 seasons of the show are what they are because it took the form (and consciousness) of somebody who wanted off the island. Whatever motivations their mother had (if she was a smoke monster) were the motivations of the woman she used to be. The reason it never exhibited any of Locke's motives (other than a few residual personality quirks) is because that was more of a metamorphosis than a birth. The Smoke Monster as we knew it was born from the MiB's dead body being thrown down the cave, and it's heavily hinted at in the same episode that his mother may have gone down there at some point as well. It taking Locke's form was a conscious effort by the MiB's personality, and thus not a true transformation into Locke.
And Hell, if their mother was a smoke monster she may not have even been the "same one". Maybe smoke monsters are like hurricanes. A woman goes down into the cave of light, 'taints' it and hurricane Mom forms. Several thousand years later, her son goes down the same cave and hurricane MiB starts brewing. Maybe if he had never killed his mother there could have been two smoke monsters on the island. Doesn't really matter to me, frankly.
To me it wasn't the Smoke Monster that wanted off the island, it was the MiB, and that made his story that more tragic. Without getting into the debate of whether or not you could even consider him to be the man he once was (if your consciousness still exists, do you?), here's a guy who's only dream in life is to leave that island but that dream actually threatens the existence of everything he wants to see out there. He's a monster and he doesn't even know it.
Or maybe he isn't. Maybe Jacob was wrong and nothing would happen if he left the island. We don't know. By giving us their backstories and making them flawed, human characters it plants that seed of doubt in our minds. Had they turned out to be two all-powerful deities as some people wanted, things would have been much more black and white.
Anyway, that's how I see it.
On a semi-related note (and back to the topic of the DVD commentary), Darlton mention that the whole temple-like plug set-up at the Source that we see in the finale wasn't there when the MiB entered the cave. I had assumed otherwise, but that would explain why Jack and Desmond didn't turn all smokey on us.