I think Ben will turn out to be a major hero. In the season 3 finale, he pleads with Jack not to call the freighter and says "this island is under assault by forces it hasn't seen in many years" or sometehing like that.
Perhaps he wasn't talking about the freighter people. maybe he was referring to nemesis. I think Ben killed Jacob or a manifestation of Jacob because he has been in on it since the beginning. It has yet to be determined which side Richard is on.
I mean, he never brought Ben to Jacob. Did he assume Ben had been communicating with Jacob or did he mis-lead him by bringing him to the cabin.
He did however, bring F-Locke directly to the statue. Perhaps he was mis-leading him and not Ben.