Nope, the other clan only attacks one clans base they dont have to attack the entire town, taking the entire town should be like it is right now, only there is a extra option to attack a clans base once you are inside the town.. Thats the point really, you dont have to take entire towns, clans have a home and they can be a pain in the ass for the other clans this way.
There should also be a rentsystem or something, to keep a base in a town, you have to pay the clan/faction that dominates the entire town you have a base in rent. The base is where you keep your stuff and troops in, upgrades that speed your crafting speed inside the town etc etc.If a strong clan takes the entire town, they can either choose to increase the rent for all the faction bases or keep it the same as the previous owners(or better yet, choose who will have to pay more who will have to pay less). See where im going with this? The faction ruling the town and the factions that have a base in that town dont have to depend on eachother. If the town gets invaded, the clans with the bases there dont have to do anything(only when its their archenemy who will raise their rent skyhigh, than that could be quite annoying). Only when its the clans own personal base that gets invaded than they have to start acting.