I agree with you 110%. I love this idea that my the Warrior does have morals even if she may be seen as a villain by others.
It's shades of gray. There is no complete black or white, good or bad. What you are doing is creating a multi-faceted character, and to me, that makes it far more interesting, and adds depth and interest to your game play.
Even though this is a game, I can totally see my Warrior as a character that people might be able to relate to. (Sans having mystical Force powers, of course! )