Spoilers to follow, but i'm not blacking these out. If you're in this topic, it's at your own peril.
To present my own idea before I address yours:
Wind Waker is about renewal. More specifically it is about life after death, about moving on after endings. You touch on this to some degree when tlaking about the King of Hyrule ending the cycle of conflict by destroying Hyrule forever, and I think that makes good sense.
The King of Red Lions and Ganondorf are both fathers - one fights for his children, one fights for the memory of his children (and his sisters, cousins, aunts). Neither mean any harm, not really, but both are willing to do grand and terrible things to honor their children: one destroys a kingdom, and the other goes mad when his monument is taken away. Ganondorf is a man who acts primarily out of grief, and his grief has colored him and the way he acts. He treats Zelda with tenderness, and though he lays Link out he levels no more force than absolutely necessary to keep the boy from interfering. He never speaks about it very much, but I think that all of his actions are driven by the memory of his people, who were lost as a result of his own actions. There's no concrete reason to think this, but I have two reasons for htinking so: in the first, he only speaks of his past as it pertains to his home and his people. In the second, he exists in opposite to the King of Hyrule.
The King of Hyrule is Ganondorf's opposite number in more ways than one. I think this is the only game where Ganondorf is not a primarily destructive force. The King of Hyrule has moved on from his grieving, has set aside his old life and all the things that were once precious to him, finding new love in the children of a new world. Ganondorf seeks to preserve the status quo, to return Hyrule to what it was before - under his fist or no. The King of Hyrule, and by extension Link, becomes the destroyer. He expels the past mentally and literally, putting sorrow out of his mind and plunging Hyrule into oblivion so that the children of his children would be able to make a new world for themselves. Ganondorf is not able to let go of his people, can find no reflection of himself or his own values in this new world, and clings desperately to the things that he once loved. He dies in the attempt.
The world is not a ruinous place - rather, it is a world that has experienced ruin and then began to grow beyond it. Ganondorf claimed there were no fish to eat, nothing in the sea that could support life, but it was not so; the people lived. His values were reduced, crumpled, discarded, and the world flourished away from the things that it had once been. Link and Zelda seeking out a new land to call home while the King of Hyrule - the last remnant of a dead age - remains at the bottom of the sea is proof enough that the intent of the narrative is a story of renewal where fathers sacrifice everything for their children, where familial duty is a paternal and maternal sacrifice (this latter best shown in Grandma when she recovers from sickness). Parents work and die so their children can have beautiful lives. The only possible difference is whether they die willingly (like the King of Hyrule) or die fighting the inevitable (like Ganondorf). No matter how it happens, the world changes, and old values are gone, and new ones spring up.
Twilight Princess, I think, was a game about death. The feeling it gave was that of going to a loved one's funeral and then returning home, happier for the catharsis but still sad.
Wind Waker is a graveyard covered in flowers and vines that wrench headstones into dust. All sorrow is forgotten; pinks and yellows and purples replace grey.
As to your thesis:
You mention Ganondorf as a puppet of the gods. Do you think that his own agency is negated by his obtaining the Triforce?
