The whole show pulls aspects from several different religious beliefs,
but is never going to be definite or follow any one belief completely.
Here's my theory:
The island can be compared to Eden, with the fake mom in last night's
episode being the angel who guards the entrance to the biblical Garden
of Eden. However, it does not follow the Eden story completely. The
tree of knowledge of good and evil from the bible has been replaced by
this cave of light. The fake mom is both the Jacob and Man In Black in
one. She decided to split these two personas or spirits from herself
into two when her new replacement candidates arrived. That is why she
thanked MIB when he killed her because she knew that Jacob (being the
good) would never do it. She also knew that Jacob would send MIB to
the light cave since she had told him how horrible it would be to go in
there. She had also led Man in Black to believe that he could never
leave the island which was not true. However, once he bacame the smoke
monster, he could not leave the island since he is alive as an evil
spirit only.
Jacob- Jacob is the "good" protector side. This does not mean he is
free from sin, but he represents morality. He was able to leave the
island and recruit his potential replacement. He has "interfered" in
the lives of all the Losties to test them to find the best suitable
replacement. Jack is the only replacement candidate that makes sense
at this point.
Man-in-Black - Pure evil; the island's Lucifer which if he is ever
named may be the name they give him. Lucifer means 'bearer of light'.
He is imprisoned on the island since he is actually dead. MIB is still
looking for his replacement also. Locke is not it since Locke is dead
and never accepted it. However, MIB wants to kill all the candidates
for Jacob's replacement and then use Desmond as his. (Desmond is not
dead just in a safe place in the well that fake Locke threw him in.) I
think MIB wants Desmond to take on both roles again so that he can
leave the island.
The candidates have to accept their new positions. This is key since
otherwise they could be forced at any time to replace either Jacob or
MIB. This is also shown in last night's episode where fake mother asks
Jacob if he will be the protector but MIB also accepts his role (albeit
through some manipulation) when he and fake mother are in the tunnel
with the wheel.
The alternate time line is a world in which since the island was sunk
due to the nuclear bomb at the end of last season no replacements were
needed and thus Jacob has not interfered in the lives of the Losties.
This may all be completely crap after the first five minutes of next
week's episode but that is the theory that I have for now.