Wouldn't it be possible to reduce points by 50% for maps with 40 or less territories
It wouldn't help. All the duel players would do is find a map that has a distribution that has neighboring start locations, set the neutrals super high, and they can do the same thing on a bigger map.
Another idea is to diminish points if the game doesn't last more than a few turns. This doesn't work either, since you could design a scenario like Duel, but where it takes a few turns to finish the game. It also opens the door for trolls who surrender on turn 1 when they don't like their spots just to frustrate their opponents.
How about diminishing points when kill rates are overridden? The whole idea behind the duel map doesn't work in normal kill rates, since it turns into a stalemate where the first player who attacks loses.