Instead of giving points based on the number of structures controled, give points base on the ranking of the three servers.
The server that has the highest control gets 3 points. The second server gets 2 and the last gets 1. That way, a server that completes a 100% map control will get a somewhat significant lead in score but a LOT more reasonable than currently. In essence, getting more territory control will give you a buffer zone before you start dropping in rank instead of a huge lead in score.