Perhaps in EU the problem is Greys or Byz massively inflating one team with extremely experienced, high level, and skilled players but in NA very rarely does a clan garner enough numbers of highly influential players to completely overcome the other clans active at the time. Even if there are no more than 4-5 representatives of each clan maximum on the server the rounds often go 4-0 or 3-1, with dozens of players left on the winning team at the end. It's simply a problem with the autobalancer.
If you removed banner balance, you'd not only make a very sizable fraction (even perhaps a majority) of the community disenfranchised, maybe enough to quit, but you wouldn't solve the problem. The devs would need to code an extremely efficient auto-balancer, and I don't think doing such a thing is on top of, or even on their to-do list at all. I don't blame them in the slightest for that, either.