Why not adopt a more balanced scoring system, where your score would be an aggregate of the following:
- Experience (but remove the possibility of colonies being set to produce "experience" - what on earth does that mean?).
- Reputation (this will put a penalty on "bad guys", eliminating the effect of pirates winning the game every single time)
- Net monetary worth (your total assets in all your colonies, both in terms of cash and in terms of buildings set down)
The reputation aspect will favor the good guys, the experience aspect will favor the pirates (as the saying goes "good girls go to heaven, bad girls go everywhere"

To give meaning to this system, reputation should be more closely linked to the morale of colonists - all "positive morale" colonies, from content up, should earn some positive rep, while all "negative morale" colonies from downcast down, should cause a loss of rep.
With such a scoring system, we will see a clearer distinction between "good guys" and "bad guys", as there will be a motive to keep building your reputation well over 5,000. Also, there will be a stronger motive for building up colonies to include all the buildings, since their value, and the morale improvement they cause, will be included in the score.
How does this sound?