The Jedi code, like any philosophical/ideological code can be interpreted and stretched in many ways. A fun little exercise I did when playing Jedi characters in the pen and paper RPG was to take the code, first as a whole, then line by line, and jot down how my character interpreted it.
As far as story goes in a galactic timeline sense keep in mind keep in mind that this game takes place roughly 3600 years before the events in the movies. Essentially for the past 1400 years, since the Great hyperspace War the Jedi have been in an on/off war with the Sith.
Constant strife and several near extinctions give us the players an opportunity to play a part in a Jedi Order that's trying to "figure itself out" as it were. So have fun play through your story and don't worry. I don't think any long dead Jedi ghost is going to appear on your characters ship and beat him/her about the head with the Jedi Code clue by Four.