I like the widening circles and their hierarchy of sophistication. Presumably, if you're really treading similar ground to your cited source material, beyond the sprawling shantytown mire there lie vast wildernesses dotted with bizarre and isolated cultures long forgotten by the folk of the metropolis.
As for the origins of magic, I would be a little concerned that nanites bear too much of the stamp of modernity to fit into a true sword and planet setting. Vance and Burroughs wrote science fantasy that knew little or nothing of computers -- in ERB's case because he predated them and in Vance's because they tend to interfere with the primacy of human ingenuity. So the leap past computers to nanotechnology seems out of place to me. For my money, some kind of rift in space and time, resulting from the unspeakable weapons of that ancient war, would feel like a more appropriate source of magic. Alien entities from beyond might have slipped through the rift, and while some would be so foreign as to be incomprehensible to man, others might latch on to the human subconscious and manifest themselves as beings that appear either godlike or demonic. These could explain both arcane sorcery and clerical powers alike.
On the other hand, you and your players may have a totally different view of nanites that would make them perfectly suitable. In that case, maybe there could simply be many different flavors or "brands" of nanites, some of which evolve into consciousnesses resembling immortal deities, and others of which remain unthinking swarms of micro-machinery, awaiting the proper commands of a carefully attuned human mind.
As far as the nanites go I see people as having a very limited understanding of them. They certainly wouldn't refer to them as nanites (though I haven't thought up a decent name to replace it with). Basically they understand that they were created by the Star Men and know that they are very useful in powering sorcery, but almost no one understands what they actually are.
I see the nanites as coming in 5 (6) different forms. At the low end there is a silvery dust. These nanites are largely inert and have lost most of their potency. By expending some of them a spellcaster is able to cast a spell without penalty. If he lacks the dust however he can still cast (at least low level) spells since the entire atmosphere of the planet is still permiated with inert nanites. The second order of potency is nanites in a gel form, followed by a non newtonian solid. These provide bonus' to spellcasting checks with the latter being both highly potent, rare, and valuable. Parallel to this they can also be found in liquid (useful for potion/poison making) and solid metallic (which forms the basis of most magic items) forms. Corruption would be explained by the fact that when activated the nanites are occasionally faulty and... well bad stuff happens.
I like your idea for gods though. Another idea I've had bouncing around my head is druids. At low levels they resemble the druids of any other fantasy campaign. As a PC gets inducted into the higher mysteries of the cult however it turns out that they are actually the decedents of the engineers who maintained (and still maintain) the ancient terraforming machines that keep the planet inhabitable.
A second idea I had was an ancient, self aware (and extremely powerful) war machine (Are you thinking OGRE? I'm thinking OGRE) that still patrols the desert of Gol-Than. A camp of fanatical followers have attached themselves to it and in exchange for maintaining their 'god' it provides direct and very real protection in addition to granting 'spells' to its most loyal followers.
I'm planning on reskinning a lot of the classes too. For example I want 'elves' to actually be the decedents of the leadership caste of the star men. 'Dwarves' (as well as Orcs, Ogres, Giants and many other humanoid monsters) will be the decedents of genetically engineered/vat grown soldiers deployed during the wars. Halflings will actually be an alien race that were the planets original inhabitants. I'm also thinking that Dragons and their assorted offshoots (drakes ect) will be native to the planet as well, potentially opening up another spellcasting class available only to 'halflings'.