Well, if a fair balance can't be achieved, a straight 50-50 split for the biggest bannergroup would be good.
But allowing people to be on the same team should have priority. Even if it means causing odd team counts like 30 vs 45.
I mean, the whole point of the banner balance system is to allow people to play together on the same team. If using the same banner would mean you'd get split into two groups all the time, the system isn't working.
Right now, i think one team can only have a maximum of 50% people using the same banner. So it all depends on how many people are using that one banner.