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In the Season 1 episode The Moth, Locke uses the emergence of a moth from its chrysalis as a metaphor for the necessary pain and struggle which the survivors of flight 815 are undergoing in order to imbue in them greater inner strength.
Locke has a relationship with his father and Helen, but as a result succumbs to the limitations brought on by his paralysis, a clear abandonment of his characteristic faith and hope. Ben doesn't bare the guilt of sacrificing Alex in the flash-sideways timeline, yet it is his contrition for such an act in the original timeline that has placed him on the side of the forces of good, likely leading to his eventual redemption.
To use Locke’s metaphor, the characters chrysalises' have been cut open for them in the flash-sideways timeline, and although their lives appear benefited for the moment, it will eventual prove to be to their detriment. The original timeline, not the flash-sideways, will have the happy ending.