A good way to keep the score in proper perspective is to simply turn off time victory, which means the game plays until someone scores a REAL victory.
That way I think of the score as the computer's estimate of how well you're doing. Which may or may not tell the whole story.
That is usually how I play, I was just trying to shut my friend up about the score thing. He's not beating that one, ever, seeing he's a warmonger that hates, and is probably incapable of, micromanagement. I got to the point where I was pumping out future techs every turn (on marathon) and had to go ahead and GDR the last capital because my population was outpacing every bit of happiness I could manage to create. I also had about 750K gold, but that gets me no credit.
Silly and childish really. But it had to be done.
I think my next game is a giant earth map domination only victory. Prove the superiority of the Aztec race.