I'm starting to think that this guy actually invented magic, or well "ancient sorcery" in the first place as part of his goal of killing the gods. I can also see why that would upset them far more than just rebelling. Imagine in, say, ancient Rome with real gods a mortal finally had enough of their shit and somehow managed to recreate divine power and in a way that it can be taught to anyone. Not only would they flip their shit, but it would completely revolutionize the world.
It would explain why the people in that academy don't even seem to understand magic. It isn't theirs. Like if you are given a piece of technology and the tools to build replicas. You can do that, but you won't understand how or why it works.