I like the megalith idea a lot! I tried to do some research, here’s what I got so far:
It is unlikely that the megalith defended itself while in its Awakened phase, because a) they tend not to care, and b) that would explicitly involve cataclysms of earthquakes and volcanoes that would mark a setting’s end. They’re also supposed to gently help their denizens thrive, and at this point the world’s state doesn’t look like it’s been helped any.
Straight from the source:
“During its active phase, a megalith can communicate […] The only mortals able to understand megalith “speech” are specialists called druids, and even they do not fully understand the process or the implications”, and later “Background: […] The home planet of all PCs is a megalith, […] The Immortals made special arrangements with this creature […] before starting to cultivate life forms upon and within it.” So what this says is that every setting with druids (and every setting period) is a megalith, although this is ‘basic dnd’ content, so it could be an outdated cosmology.
Of interest is the bit about gods making arrangements with it before making life there (supposedly because, before hibernating, the megalith rotates with increasing speed until it’s discarded everything on it, lands and life included), yet there are no present gods in Dark Sun.
Also, their average density is anywhere between dry clay and solid iron+, so we can’t make any deductions based on the low metalic content (the heaviest of materials).
Off the wall theory:
So, pre-blue age, Athas was a very standard and goded planet (let’s call this the Awakened Age). At some point, the megalith Athas decided it wanted to nap (in an event we shall call the Dormancy), and began the spinning-dispersion process.
The advanced tech-magic of Awakened Age populations (on par with the terraforming tech-magic of the blue age or higher) allows the denizens to delay their doom even as the heavier materials of the crust are slowly torn out and flung (because they would get their gravity overcome by centrifugal force first, as in lab tools today, tl;dr metals and rocks shooting out of the earth into space), and the situation gets progressively worse.
The gods then intervene, forcing an end to this either by fracturing the Megalith’s spirit into the spirits druids today commune with, at the price of their life, or by killing the Megalith and changing their nature into replacement life forms, as modern druidic spirits.
This ends the calamity, but at supposedly high loses of life, civilization and technology, and most importantly, of material. The heavier the material, the least of it left and vice versa. Most of the material left is water, followed by typical soils and only the smallest quantities of metals. This leaves our familiar metal-poor planet behind, but most of the mass left is water, and as the suface settles, most of it is covered by vast oceans. Welcome to the Blue Age.
In an effort to repair the damage done to life (mostly nonsentient), the Gnomes focus research in the fields of life-shaping, that was most advanced at the Blue Age’s dusk. Generations later, they decide the sea will need to host more life, being the most of the planet’s surface. The rest is history (or rather, legend).
Ok, so this is 99% a pile of crap, but it is crap consistent with what little we know