You just stop allowing new players from Yak and Darkhaven while the third server has a very low population. Population imbalances are impossible to code around and still making game fun – Blizzard tried it a few years ago with Wintergrasp in WotLK and they ended up making the match a closed one precisely because no matter how much they buffed the side with few players the match was always won by the group with the most population. It just isn’t practical to have a battleground zone where population isn’t at all controlled.