Right now, Yergius will let you train certain skills with him, and that's it.
How about there be a new NPC, deep within the CoC (say, a couple of floors below the Air Temple), called the Chaos Guru. This guy's head has mutated to have an exceptionally large cranium, which, as you can probably expect, makes him exceptionally intelligent. He's also quite crazy, but his high intelligence allows him to keep a tight rein on his insanity.
The Chaos Guru would essentially be the ultimate version of Yergius. Acting kind of like a Potion of Training, you can spend time training with the Chaos Guru. You can't choose which skills you train, but time spent with him in deep meditation will significantly boost a few skills. The downside? Well, it takes some time, and you ARE on a deep CoC level. But even if you used Scrolls of peace to eliminate corruption on the level, the mental connection with the Chaos Guru would naturally corrupt you - essentially, corruption while meditating with the Chaos Guru is given at the rate defined by that level of the CoC, irrespective of the current danger level.
The control you do have is over how long you spend meditating. A longer duration is better, and trains more skills as well as training them higher.
Perhaps the Chaos Guru can also teach the player certain skills if given a particular artifact. A natural choice would be the Black Tome of Alsophocus, although the Crown of Science would also be a good fit. Another option could be the Weird Tome, which would therefore not be able to be given to the Mad Minstrel. The skills could, perhaps, be some of the ones that you otherwise can't get except by luck/wish or by Race/Class. It could be some subset of, say, Alchemy, Alertness, Concentration, Cooking, Gemology, and maybe Music. Of course, by that far into the game, you're not likely to have too much use for any (except maybe Alertness/Alchemy combo for DV bonus, wrong alchemy explosions, and evading bolt spells), so it's mostly a way to use up an otherwise not particularly useful artifact (Crown of Science is good pre-ToEF, but I don't see it being of much use that far down).
He wouldn't consort at all with Lawful PCs, and training given to Neutrals would be significantly less effective (relative to time spent) than for Chaotics.
Perhaps there could also be a "save the Guru" option, where you have to find some way to heal the Guru, much like Yggaz, with some sweet reward. I'm thinking that perhaps it could only be available to Champions of Law, and could perhaps require that you take him to a converted elemental altar, or something. Of course, this would be hard to do, especially since you'd have to lure him to the altar in some manner.
OK, last issue - what happens if you attack and/or kill the Guru? Well, I figure that the first property is that he'd be a karmic being, but also a chaos being. So all the effects of both would come into play. The Guru would have very high DV, but no PV at all, and low hitpoints. He would have a corrupting attack, he would be immune to all four elements, he would drain Learning and Willpower, and he would cast confusion and elemental bolts. He would be vulnerable to Human Slayers. His corpse would grant all four luck-based intrinsics (Doom, Curse, Lucky, and Fate Smiles), would corrupt massively, and would give a large boost to Learning (say, +6). It would also draw the player's alignment strongly towards C- (so strongly, a crowned champion of Law would come close to becoming a fallen champion from it).