Well it's been a long while since I posted a theory, well I have a theory based around the dirty water inside the temple.
Baby Ben was obviously taken to this water, and then healed by it, we can tell this much. Did it corrupt him from thereon? Maybe.
Okay so why is the water there dirty? Well, when Keamy killed Alex, this caused Ben to become infuriated and resort to the last defence mechanism he had, to release the summon the smoke monster - or, not to summon it as such, but to play his part in altering the course of the smoke monsters future by draining the water in the secret doorway. It just drained away. Or did it?
No, I reckon this 'tainted' water went down a long channel somewhere and into the purified water in the temple, ensuring that the pool could no longer resurrect people in a way that was pure, it would ensure the smoke monster would absorb them. This is probably why they bury people because unburied ones can be resurrected by the others and unwittingly borne unto the rule of the smoke monsters dark heart rot.
Why did this happen though? Well, it ruins any chance of people being healed, they are supposed to die and be resurrected anew and join the others as those who have died but were born again through the holy well spring. Now only evil people are resurrected using the well, which really stops all chances of people being resurrected, could jacobs ashes have been resurrected? This is probably why smoke monster burnt jacob so he could never be restored.
When the Frozen Wheel is turned do you think this could sink the island? I have a feeling that when the island is 'moved' it is not moved through time but underwater, and when we saw it disappear it actually dropped under the ocean during the time when Locke turned the wheel for the final time. This would never have happened if Jack and everyone left of course.
When Locke turned the wheel that time a time where the island was underwater may have been created? This bit is really an extension of my main theory and sounds like a load of rubbish now I've written it. But yes, that well of water behind that door I think tainted the holy water and thus makes everyone who comes to be resurrected turn out evil needing the others to kill them properly.
The end! (What are your thoughts Lost fans?!)