It kinda sucks that the banner balance seems to get abused. A solution similar to what Thomek suggested might work.
Personally, i really enjoy having the banner balance. Without it, i have to fight my clan mates all the time, which sucks, because we like to play together, not against each other. So removing it is not an option, if it was up to me.
I hope the devs have the time to work on this. Until they do, i'd like to ask those concerned not to abuse the banner balance. If it's really bad, consider getting an admin to come look. I play battle mode mostly, but i'm always on irc.