Hello! 

 

I've decided that I made the "wrong choice" in the Council of Stars -- I'd like to talk to the God I'd agreed with, say "Er, hang on a second, actually <this> is a better idea", and carry on with the story. 

 

Of course, an in-game option doesn't exist to let you do this. 

 

Does anyone know of a console command to manipulate some variable to unset the fact that I've agreed to serve Hylea? 

You can change if you just talk to them and agree to serve in their name.  

Yeah, you can change them back and forth until you descend into the pit. All you have to do is pray (and do their quest if you haven't already)