First Fix for Zerging. One thing that might help fix is titles that discourage it. Titles such as Castle Defender or Garrison Defender. Other titles can include such stuff as Cannon Master, Siege Destroyer. You can go on from there. Make more rewards for people who successfully defend a point from the enemy.
Second fix for Zerging. Make a cap of some kind on the experience you get from running around in a Zerge. People will not want to Zerge if the experience receive is split up between each of the players involved. I/E if a player is with 100 other players taking a tower down, the experience they get will be divided up between a 100 players. Stops people form leveling their Characters through the Zerge. Which from what I have seen, is why allot of people do it.