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He stayed back to "work some things out." That could include being with Alex and Rosseau, but it generally means that even though he was welcome inside the church (heaven), he decided to think about what he'd done in life and wait outside the gates for a while.
That ending for Ben is perfect to me, since he clearly did some evil things, but ultimately wasn't an evil person. He did some redeeming things towards the end of the series, and presumably gave a life of pure service to Hurley and The Island afterwards.
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