[WW] The gods didn't flood Hyrule, the Royal Family did

In the beginning of Wind Waker, we see a story about the drowning of Hyrule which says that the people prayed to the gods, and they sent the flood which sealed Ganondorf. But in that picture, we see them praying to a complete Triforce, which should not be possible at that point. Ganondorf still had the Triforce of power, and the Triforce of courage was shattered when Link was sent back in time.

So unless they somehow managed to steal the Triforce of power from ganondorf and someone reassembled the Triforce of Courage before breaking it again, there was no wish on the full Triforce, nor even a full Triforce to pray to.

But the Royal Family still had the Triforce of wisdom with them, and that is able to immensely increase the magic of its user. With the greater part of Ganondorf's power still sealed in the sacred real with the Master Sword, the Triforce of wisdom would be largely unmatched, and likely the most powerful object in the world, the one thing most capable of sealing ganondorf and hyrule under the sea (Water which is often associated with Nayru and the Triforce of Wisdom.)

Okay, but maybe the Triforce was just supposed to represent the gods. Except the golden goddesses are pretty much entirely absent, and seem to only interact through the Triforce, as was established in Skyward Sword. We don't see or hear about any specific gods of significant enough power to flood all of Hyrule during the game. And even if it was a coilition of lesser gods, how would Ganondofr not overpower them when he gets his full power? Why would he have to wait to wish on the complete Triforce, unless the flood was established by the power of a piece of the Triforce? The only other time we see the "gods of Hyrule" mentioned again is when Ganondorf was making his wish on the complete Triforce at the end of the game.

tl;dl - The Triforce was not complete during the time of Wind Waker's prologue, so the Royal Family used the Triforce of wisdom to seal Ganondorf by flooding Hyrule and blaming it on a decision of the gods.

Are there any objections or counterpoints to this that I missed? Is there any other evidence of the gods of Hyrule being able to overpower even a single piece of the Triforce?