Perhaps as the leader of the militia, the region lord could chose a banner for his region that is displayed for the militia or that region and any knights of that region not assigned to an army? It seems to me that the militia's loyalty is to the region and region lord not to the realm or the crown.
A banner for rouges would also be nice. I also think that the ruler should be able to set the banner for unaligned nobles
Army Banner - Displayed by units a part of an army (If set)
Rouge Banner - Displayed by rouge units
Region Banner - Displayed by militia of a given region and knights of that region not assigned to an army.
Realm Banner - Displayed by unaligned unites of a realm.
