Re: Maybe Ben can't see Jacob...
This was my thought as well. I'm just going out on a limb here, but suppose there is a prophecy of a island-style messiah.
Ben may have been using this prophecy to lift his position among the "Others." Suppose that one of the elements of the prophecy is that the "chosen one" will kill his father. The hostiles could have used that prophecy as an inducement to get Ben to betray the Dharma folks.
Perhaps Ben has been riding this wave for years, and along comes Locke. Maybe Locke has fulfilled other aspects of the prophecy and Ben feels threatened. That could have been the basis of the otherwise bizarre scene where Ben tries to embarass Locke that he can't kill his father. I also think Ben secretly suspects that Locke is the chosen one.
Maybe that's also why Alpert is helping Locke. Alpert knows that Ben is a pretender, because Alpert is the one who fooled him into believing that he's the guy.
I think that when Ben found out that Locke could hear Jacob, it cemented it all in Ben's mind. Ben finally knew for sure that he was a pretender and that Locke was the chosen one. That's why he shot Locke - to protect his position with the Others.
Of course, this is all just wild conjecture. But, it's fun to guess.