I only got to see the first 15 minutes of tonight's episode before I got called in to work, so I had quite a bit of time to think about the things up to Claudia's ghost appearing to the Boy in Black.
I got to watch the rest later, and it seemed to confirm my original supposition: I think Mother knew most of the things that were going to happen and she tried to change them, as many have theorized Eloise Hawking has done/is doing.
The part that I kept playing over in my mind was the twins' birth scene. Specifically, how Mother looked at the second twin (The Baby in Black? Now that's just getting silly) in such a surprised manner. It was like she both expected him, and didn't at the same time. Then, she abruptly kills Claudia. Why?
I think it's possible that either being the "protector" has a certain prescience involved (which explains some of Jacob's actions) but not total omniscience. Perhaps Mother knew that one day a pair of twins would come to the island and something would corrupt the younger one, which would lead to all the things that we've seen come to pass.
But in trying to prevent his corruption, by doting on him, telling him he was special, giving him gifts, Mother only ensured his corruption. Maybe the universe course-corrected by way of Claudia's ghost. Later, when Mother is giving her position to Jacob, she tells him that it was always meant to be him, despite her seeming to originally favor his brother for the job. (A nice dovetail with Sayid's last words last week.) It seems as though she may be resigning herself to the fate she caused.
It's even possible (and this is probably too far-fetched for only 3.5 hours of show left) that someone directly told her how things would play out. Maybe she somehow found out (possibly from the previous protector) that one day, a woman would come and give birth, and there would be twins. The younger would become evil, try to leave the island, and threaten humankind and the world itself, all because his mother drove him to it. Mother may assume that she's doing the right thing, killing the child's mother, and is totally unaware that she herself is the mother referred to in the prophetic message. And suppose the message also said that the older twin would "kill" the younger? I'd think that would make her want to set some rules to prevent that.
Which leads me to my complimentary theory: The Boy in Black says (oh so subtly) that one day Jacob might get to set the rules to his own game. That led me to consider this: What if the rules are made up by the protector, and not actually something set in stone somewhere? For example- candidates. Mother never mentioned candidates. How does all that work? The boys being unable to hurt each other (which doesn't seem to work very well anyway, as Jacob keeps beating MIB up throughout the episode). Neither boy can leave the island, yet Jacob still gets to go around and have chance encounters with all the candidates.
Maybe Jacob kept some of the rules set by Mother and made a few of his own up. Like MIB can't kill his candidates, he's allowed to leave the island while MIB still can't, MIB can't just up and kill Jacob, since that wouldn't be very good for a show with 6 seasons, etc. It seems that being a protector may come with more perks than just immortality and snappy all-white fashion sense. Maybe as long as they stay on the island and protect the "source", they can do pretty much whatever they want.
Hell, they may even be able to fart fire and kill with a thought, after seeing what Mother did to the Romans' village.