With the upcoming update hopefully making the siege system more combat based instead of just ramchecking your camp every 24 hours, there is a possibility that the game is going to suffer from the opposite extreme, which is making it too easy for the bigger and stronger botters factions to win over smaller groups of players. The best way to balance it out of what I can think of, is making it so the town walls would provide the defenders some sort of combat advantage over the attackers, just like it was in the medieval times - the whole purpose of building city walls was to help less trained and poorer equipped townsfolk standing against regular armies.
So here is how it can be implemented:
1. Defenders buff - all the village members within a certain radius around the village idol get their combat stats significantly increased for the siege(or permanently, because I don't see how it could hurt anything).
2. The defender's archers are allowed to shoot through walls and obstacles and perhaps deal higher damage.
3. A combination of 1 and 2.