Time for some major facepalming! I've been re-reading the MRQ books a bit more closely and there are some major hints that the God Learners are messing with some fairly dangerous stuff:
Students HeroQuesting myths where they take the part of Chaos gods, myths where uz gods are Chaotic, making new gods etc.
CultsII says that many Thanatar temples are close to GL centers of learning.
I disagree. I'm thinking that in many (if not ALL) cases, the Thanatar temples ARE the centers of learning.
1) At the dawn, there are two cults, each a part of a dead chaos god. Then, somehow, they re-unite. That sounds like God Learners in action to me. The stuff that Mongoose has published has already established that the GLs have created at least two new gods (Zistor and some other, unnamed, god in Pamaltela IIRC). Taking Than and Atyar and recombining them sounds right up their alley.
2) Thanatar steals knowledge. Wouldn't that just appeal to the GLs? Why bother trying to worm your way into the confidence of some smelly barbarians, when you can just cut their heads off and take what knowledge you want.
3) As for the requirements/geases to eat sentient flesh? All you'd have to do is go down to the slaughterhouses and, under the guise of "blessing" the livestock, cast "Release Intelligence." Like some ignorant pig herder could tell the difference.
4) Ram's Horns? "Yes, poor Tompkins. Got caught in the backlash when a spell went awry. Well, these things happen and it's all for the greater good. Someday he'll have to get rid of them, of course, but for now ..."
5) Chaos? All good GLs know that chaos is just primitive superstition, it's not real. Yes, they cut off heads and imprision the souls, yes they devour books, yes they sacrifice POW to Thanatar/Than/Atyar, yes they steal knowledge, but it's not as if they really MEAN it.
There is another thread about what cults are on the covers of CultsI and CultsII. I'd say that CultsII shows a God Learner academic with a couple of undergrads.