Overall great theory, but I know something that makes it wrong. The gods flooded Hyrule, not an earthquake. I think they flooded it so hyrule could no longer be harmed or something along those lines.
Oh wait, I just found Daphnes Dialogue from windwaker:
"Once, long ago, this land of Hyrule was turned
into a world of shadows by Ganon, who sought to obtain the power of the gods
for his own evil ends. My power alone could not stop the fiend, and our only
choice was to leave the fate of the kingdom in the hands of the gods... When
the gods heard our pleas, they chose to seal away not only Ganon, but Hyrule
itself... and so, with a torrential downpour of rains from the heavens... Our
fair kingdom was soon buried beneath the waves, forgotten at the bottom of the
ocean."