I subscribe to the "Ganon Battery" theory. If you look at the source of the hand on the ceiling, it looks like there are 5 little Sheikah "tips" sticking out. These are most likely the start of the 5 pillars that rose from the ground when Ganon attacked, probably activated by his malice emerging deep within the castle.
There is also a series of what looks to be wiring, or primitive stonework, at the source of the green hand. We know that Hyrule Castle acts as a central hub for the Sheikah technology, what with the Astral Observatory, the 5 pillars, and the source of the signal for the Sheikah towers (as confirmed by Master Works). And at what is presumably the deepest depths of Hyrule Castle (as shown by the raising of it in the second trailer), we see Ganondorf's body being held by a Zonai spirit-hand feeding into a network of stone wiring. Fishy fishy.
The green hand is harnessing Ganon's power to power the Sheikah technology. This is why Malice can so easily corrupt Sheikah technology. The Zonai energy converts Malice into the blue energy we know. Which is a, um, not good idea. And probably was one of the reasons for the Sheikah banishment; because their technology is literally dangerous. We also know that the Sheikah at the very least converted Zonai relics into Sheikah-based artifacts (Thundra Plateau, Thyphlo Ruins, the three labyrinths), so they may have done the same with the ruins below Hyrule Castle, or directly helped the Zonai in the sealing process.
To the original theory raised, that seems plausible. By mummifying him, I guess it prevents reincarnation as Ganondorf (like what happened in FSA). But they did a shoddy job sealing him up. The theory that there was a war with Ganon and the Zonai is interesting, but I think it's probably the Royal Family and the Zonai. Having another powerful kingdom with more powerful magic probably wasn't great, so the Royal Family likely wiped out the Zonai to keep a grip on power in the subsequent years after Ganondorf's sealing.