I had the same interrogation as you Aemaelius, but not the same conclusion.
I think it would be too bothersome to have a Banner Balance WITH a kind of Class System that would make the game more balanced in terms of numbers of footmen/archers/cavalry in each team.
How about adding a Class System Balance to EVERY SERVER that will exclusively balance the numbers of players having RANGED WEAPON and/or HORSES, without even thinking of the banner ?
Then every admin on every server would be able to choose between FUN MODE (banner balance, permits players to play along their comrades) AND SERIOUS MODE (class balance, permits everyone to play against a balanced team).
When the balancer banner fails SO MUCH that the fun isnt there anymore (like OP said, when a team has far more cav and/or archers), we would be able to switch to a more enjoyable balance, even if clanmates will have to kill each other (I think it's not too great a price when we are talking about a a 100 man server).