Debating on these very forums someone mentioned that the ending had nothing to do with the show as a whole. The afterlife just popped out of nowhere in the last season for no rhyme or reason. I was inclined to agree at first, but then I started thinking.
Forgive me if someone mentioned it before or if it is common knowledge and I'm just dense for piecing it together now. But what if the EM anomaly at the heart of the island IS the afterlife. We see when Christian opens the church doors, a bright light. We all know that the "afterlife" is usually described as a bright light. Perhaps the warmest, brightest light you've ever seen or felt IS that afterlife.
Mother mentions that the light is life, death, rebirth. Rebirth could be after your life, and your death, you are reborn in the afterlife. This may mean that The Source is more than JUST the afterlife, but I won't delve into that for fear of confusing everyone (and perhaps myself).
Using a heaven/hell analogy, Desmond pulls the cork out, which extinguishes heaven. We then see some hellish fire in heaven's place. Jack puts the cork back, essentially saving the "souls" of everyone in the afterlife. He always wanted to save everyone and perhaps he did.
I'm not even sure I agree with my own theory, but it does tie the island to the ending. Darlton did say that the show is ultimately about the island. So it doesn't quite make sense that half of the final season had nothing to do with the island. With this theory, the final season is ALL about the island. Food for thought at least.