[Outsider Chronicles] Thematic Conflict

Save the Ship or Follow the Prime Directive?
Follow the School Rules or Break Them to Save the School?

While working on the Outsider Chronicles, I had it suggested to me that it would probably benefit the game if the generic Luna system were changed to fit the common adventure format of the game.

Most of the Outsider Chronicles adventures will be of a mission-based variety. Something goes wrong in the time-space continum, they fix it, and come back. However, if you pay enough attention to the structure of most fiction, its never that simple. How many times has Captain Kirk broken the Prime Directive in order to save his ship and crew? How many school rules has Harry Poter broken in order to solve a mystery at Hogwarts?

Character in these types of stories often end up pulled in two different directions on an almost constant basis. Does one follow the Establishment or do you fullfill your own goals? Both have their benefits.

The question is how to represent this in a game. I am thnking along the lines of experience points... Mission Points, which are gained by successfully fulfilling the goals of a mission and can be spent on things that your job can give you.. a better position, more money, better equipment, etc. There could also be Personal Points that the character would get for fulfilling his own personal goals that my run counter to the mission's goals. Personal Points would be spent on things of the non-job variety.

If anybody has suggestions, I would love to hear them.