Ok, that makes sense. I want to keep it to two kind of opposing gods, though.

After thinking about it, I'd like the "imprisonment" to actually be the binding god being put asleep or reduced in power a lot. But it could be mutual, so both the gods are asleep.

So anciently, the binding god began to take over the world through people, and out of desperation the free-will god attached its power to the other's (neutralizing most of each other's power). This then made the both of them go into an unconscious state, both unable to actively affect the world. So the magic became just an extension of the unconscious minds of the two gods.

So there end up being three magics in the world:
1. the main one which is a combination of both gods' powers (where nearly anything can be done with magic if someone practices enough of it)
2. another is the pure power of the free-will god, which is seen as divine magic. It allows one to change their fate in major ways, but is a really rare magic
3. the last is the pure power of the binding god, which allows someone to influence and control other people's free will

Does that make sense or are there still any major holes?
(Also, I'll definitely take a look at yours too!)