I agree that the banner balance system is a nightmare for players who aren't in a clan. I took a look at the code to see if I could do anything, but it's too complicated and long for me. What I had in mind is count "group players" as more than 1 player, so that clan stacks would end up having less non-affiliated players than the other side, so that the teams would be uneven in total. I think this would still be fair, because a) clan players are in average more skilled than other players and b) clan players often have voice communication, giving them a big advantage over other players.
My idea was to find a formula that would scale effective playercount based on the size of the clan banner group. E.g. if only 2-4 players form a group, they might be counted as 1.1 or 1.2 players each, and if player count in the group went up, it would count them as 1.3-1.5, approaching, but never reaching 2 for the very large groups.
Other people also want to take class into account, so that cav isn't massed up on one side, or ranged, but I think this will become very complicated, probably unsolvable.