The Hurley in the church is a future Hurley who had already spent an unspecified amount of time as the protector of the Island along with Ben Linus as his assistant. Presumably changing the rules and doing a good job of it (since Linus tells him 'By the way, you were a great #1'). In fact, in retrospect, it's pretty clear he was acting in a 'Jacob' role in the sideways universe for the last few episodes.
Remember, as Mr. Sheppard told Jack, "There is no 'now' here", meaning that the church exists independently of time. Presumably all the people in the church had lived full, rewarding lives prior to showing up to 'move on'. It's just that these events were merely hinted at, and not actually shown to the viewers.
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-Bumamgar
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