I seem to be one of the few who were immediately satisfied with the ending of Lost. Although the abruptness of the reveal (the alt.timeline showing its true colours)did shock me at first, I nevertheless felt that what we were seeing - the main island timeline and the waiting room of dead souls - were more linked that evident at face value. Here is why:
Throughout the season MIB has threatened to leave the island and we are never given a clear reason as to why this would be so catastrophically bad. Widmore and others assure us it would cause everyone the characters love to "simple cease to be". Many theories picked up on this and suggested there was a significance in the choice of words (rather than saying "they will die"). "Then we all go to hell" was also said, and I do believe these words are the key as to what MIB leaving, the cork Jack puts back in place after Desmond disengages it and the dead souls waiting room have to do with eachother.
In Happily Ever After, Desmond is shocked with a massive ammount of electromagnetic energy (light) and experiences a glimpse of the waiting room. However, although he tells Jack that when he enters the cave the same will happen we learn that this is not the case. The reason for this is that he unplugs the cork.
The cork is keeping the light in place and maintaining it. This light is the same light that bursts through the doors of the church in the final sequence. If MIB destroys this, then everyone will "cease to be", as when they die they will be dead and nothing more. He is destroying the possibility of afterlife.
("We all go to hell" Nothingness is pretty bad when compared to an existence beyond waking life, therefore a form of hell.)
Science VS. Faith comes into play in relation to MIB leaving the island. If he does, he will be discoevered, studied or more simply tell people about the island as he does not care what happens to it. If he does this, the scientists of the world will analyse the light/ energy as atheists. They will not fear or understand the reprocussions of potentially destroying it as they perceive the concept of an afterlife as false. This is why he can never leave and if he does why everyone will "cease to be". Again, they would just die and that would be it. Dead would be just dead. The message becomes: science has given us so much, but when it collides with faith what are the rammifications? This is a literal example of how they cannot exist in the same world.
Jack's turnaround has been nothing short of spiritual. He commits to becoming the new Jacob and to believing he is supposed to stop MIB without any real evidence (science). The reason he does not need this is because some part of his being realises that the fruits of his labour are more important than anything science has ever taught him. His task is to preserve the afterlife by killing what is a threat to it, MIB, and ensuring the energy is maintained qhile sacrificing himself at the same time. Had he not made this sacrifice, there would have been no afterlife for anyone, not just the islanders.
Christian did say that they created what seemed at first to be the alt.timeline. However, it merely took that form because of their shared experience. In the world of Lost, if anyone dies(even off island, never having heard anything about the island itself) they would too have entered a similar scenario in which the most important people in their lives were present. They, like the losties, would all have to remember eachother and their respective deaths and experiences in order to let go of their previous lives and move on. Jck ensured this would happen.
Glimpses of the energy under the island being representative of the afterlife are evident through the various ghosts/whispers and other paranormal occurences. They are slight gimpses or flashes of this other world.
Thanks.