I think that the score might be calculated as [(faction_population) + (4*time_remaining_for_victory) + (something_else)], where time_remaining_for_victory is calculated as (1000 - turn_number). something_else might be bonuses based on what victory types you had, or the difficulty level of your opponents, or something along those lines.
However, the above is a guess - I'm not sure that that is how it is calculated, and I don't have a large enough sample size to determine if that really is about right or not.