Here we see a John Sheppard who has given up on himself. Unlike the more familiar Sheppard, this one has found only loss and failure from his attempts to "go back in" and risk himself for others. He is rejected as a failure, and rejects himself, although not completely successfully. In his meager accomplishments he betrays his true character, and displays his inner, perhaps unconscious conflict.
He is given an opportunity to grab an easy fix for his life's problems, at the cost of not risking himself for others, in what he already knows is likely to end badly for himself. This John Sheppard has been taught very different lessons from life and expects very different outcomes. In his choice we see a redemption of John Sheppard, and an affirmation of the Sheppard we know in a way that could never have been accomplished with the slightly comic action hero we have been shown.