Sorry to necro this, but we just started playing this. We scored by only including resources that we still held. (We did not include citizens or goods that we had to supply to the city.)
It's not perfect because my individual goal didn't call for much progress on the development track, so I scored far fewer points for the team. My partner had a personal goal of progressing their development track to level 6, and also built several buildings along the way to fortifying the city.
We would have lost the whole game had I not done my thing (I put every knight on the wall, for instance) and since it's a team score anyway, that's cool.
I'm no mathematician, but we thought that was a fun/simple way to score our victories.
That sounds interesting. Would you score resources even if they had been part of a player's required goal?