This is becuase MiB is always there, Jacob was a mere 'prison' guard if you like, nothing amazing, as said, a demi-god, so he can be killed. We don't know why Ben could kill him and MiB couldn't. If you remember in the 1st season, Locke sees what he described "A white light of beauty" or something simliar which was the white smoke monster, yet to see. This also fits in with the black and white stones we saw in the cave and also the recurring theme of black and white, if you remember Locke's eyes in Claire's dream, one was black one was white.
The writers are writing a "LOST encyclopedia" which aims to answer some unexplained questions as they didn't have time to answer them all in the show. They have said they will answer the Hurley bird though, amog with a lot of others.
Yes I know there are children on the Island, Apep's wife is Goddess of child birth (would show why children cannot be born), not children.
A lot of people think Aaron is Jacob/MiB. Can't wait for this weeks episode.