The thing is that those playing in an extremely casual and/or intentionally disruptive way have paid for the game just like everyone else has, and would probably not be happy about being labelled or "numbered" based on their extremely casual/just-messing-around playing styles. If you pay for a source of entertainment you don't do that to be judged by it later on. Nobody states on the game's website or on steam that "this game is only for those who mean to play nicely and seriously, and will learn everything about game mechanics, and will always contribute their best to the team, and listen to their captains, or else we'll give them a low score and booom, so much about being respected by the community!". It's another thing that the game has its own policy of conduct, and players violating that can be held back from the game through an official process (you automatically sign up for that condition when you buy the game and accept the terms).
Also, if the score system that you suggest is based on players' judgement, how can you make sure that some players won't use it to abuse novice players/anyone else because they messed up something during their matches? A raging captain would hand out low scores to all of his/her crew at the end of a bad match. Will players have the right to protest against those points and say "I was doing my best, I shouldn't have received those points"?
And then imagine what would happen to a guy with a very low score in a lobby. People would start hating on that player immediately, and this system would not even give a chance for a "second start", at least not immediately. Let's say somebody manages to talk to the trolling player and ask him or her to stop it. Let's say the person actually agrees, but can't start it with a tabula rasa because the scores say otherwise.
I think we have ambassadors, the leave counter, the commendation system, the block system, even a report system. We also have tools of communication to talk things over. All these should be quite enough to solve in-game issues. If still not, you can always switch lobbies, mark players you dont wanna play with, and avoid them easily later on.