The Story Arch should be the main quest. The side quest should be the submissive quest and would normally be an option for achievements and not affect the main quest, like most other games.
So, if you want to play the submissive fool, then you can choose the option to do the side quest. Wouldn't it be satisfying at some point where the MC says NO, and kicks the ghost, or demoness or whoever in the ... you know. :D