Taken at its face value, the scene at the church is a mystery. The 'Losties' meet up at the church which happens to be above Eloise's Dharma Initiative Lamp Post Station. In an episode last season before Jack and Co. returned to the island, they met with Eloise who chartered the course and flight route to return to the island. Now they have reached a 'consciousness' with their significant other (Jack/Kate, Sawyer/Juliet, Des/Penolpe, Hurly/Libby, etc.) and has a reunion of souls at the church.
What I have difficulty understanding (and I wonder if the Lost fans here know) is comprehending Jack's dad, Christian, when he said:
Christian: "This is the place you all made together so you can find one another. The most important part of your life, was the time you spent with these people. That's why all of you are here. Nobody does it alone, Jack. You needed all of them and they needed all of you."
When I heard that I went 'huh' and led to more questions. Who built the portal to the afterlife? Before reaching the final stage, the Losties were all on the island - they didn't have the time and were 'not ready' to go further in their purgatory/alternative universe. The rest of the sentence makes sense - the theme of 'live together or die alone' is stated in Christian's words which is evident throughout the series.
In the end, I am satisfied in the outcome of the characters that we all got to know. Maybe some plot twists and elements of the show have to be that - a mystery - like the briefcase in 'Ronin' or as stated in another posting about the Marsellus's case OR the writers and producers rushed the metaphysical/spiritual aspects of the show to close out the series. Hopefully there will be an enhanced episode. For now I'm going to try stop asking 'why' on this and other questions (i.e. the cork, the numbers) and follow Christian's advice and 'let go'. Thanks for having this forum to air my thoughts out loud.