Ben shot Locke in the gut and left him for dead because he was jealous of the Island's favoritism for Locke. Remember his dialogue in the finale indicated that he was lying to the other Others about hearing Jacob. Locke actually heard Jacob! Obviously Ben has taken a "keep your friends close but your enemies closer" attitude, and I have absolutely no doubt that he will betray Locke down the road. Just wait for it. Don't trust Ben! I certainly would not say that he knows the right course of action or that he believes Locke is pursuing it.

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“Because, in a land of predators, the lion never fears the Jackal.” – Dexter S3E03 “The Lion Sleeps Tonight”