You know...thats a dam good question as i was wondering this too
I would assume...based of older mmo's and other similar systems...is that you'll either:
-Be completely unattackable whilst your/there logged off or
-You will be worth no points or honor or w/e and the attacking player or you will be punished for attacking you/them (then again that wont stop people)
-Your/there base will completely dissappear and be replaced with maybe some kind of "no go" zone or some kind of restriction or w/e
Or...something along those lines, i dunno.
Because it would be weird wouldnt it, for when you go to "expand" your base, all of a sudden someone logs in on the deceptively empty peace of land you want to build on... and a fortress suddenly appears from from above your 2 workers and squash lol or...you would walk into an area and it would go "You cannot build here...this spot is reserved" or something...be kinda annoying.
It it worked like that or something...you would need the world map to be absolutely MASSIVE and maybe you can only build in your factions "province" and if you try to wander in to some other province you get like...border patrol or endless spawns of guards and warning coming at you, or maybe theres actual physical preventions from you simple straying into another players territory or w/e...then again what about other players in your province...hmmmm
OH! Unless...there are forms of "instances" or "battlegrounds" that you participate in to attack other players or something
Well I simply dont know how it would/will work. If players of the same faction are automatically freindly towards each other and oppossing factions arent then...i guess that would be slightly easier but some what limit the playability
Lol well hopefully someone can reverie can help clear it up