I have just listened to the developers on tea time speaking about alliances and discussing population balance and rewards. Another game I am playing at the moment (Planetside 2) has faced similar issued described and their solutions may be of use:
"Alert" System:
This system involves a bonus event on a certain map where 3 teams are given a certain amount of time (1hr 30m) to control the most bases on the map. This event can be triggered either by a certain team controlling too much of the map or by a certain amount of players being active at a time e.g. prime time. Players are then rewarded for playing during this event based on participation with the winners getting a bonus reward.
Dynamic Rewards:
With dynamic rewards players who are active in a team with lower population are given extra rewards. I guess this is similar to outnumbered which is already implemented. However outnumbered is map based rather than global.
Restricting Play Space During Off-Hours:
This could be freezing the borderlands and the points gained from them when a certain population threshold is met. Forcing people to play on EBG during Off-Hours would funnel people together and allow for more populated fights.