I assumed that when Desmond pulled the plug on the island it activated the dormant volcano under/on the island and thats what was happening, the volcano was about to erupt. And the electromagnetic energy was somehow harnessing the volcano and stopping it from erupting.
The volcano has been talked about by Darlton before now and it has even been referenced in the show during season three.
The volcano may have been the way in which the island was destroyed, but I think the point was that the island/cork was acting like a cork in a bottle, stopping evil (wine metaphor) from escaping into the rest of the world.