k now I read Malicewolf's explanation (thanks!) and re-read edited original text.
so, basically, along with clans, you suggest to make Factions, with between-factions PvP
so, what could be said to that:
1) 2 factions is too small number (and it will cut away 50% of players from your opponents list), how about 4 factions instead. Not only its more chaotic, temporal alliances between factions will allow temporal "2 factions" event
2) Factions and clans. If ppl from clan are all in different factions, it would be not good. Either "civil wars" (between clan members) everywhere, or peace between factions (again, withim same clan). So I suggest, if factions are implemented, all clan members are required to be in same faction as their clan leader.
3) Faction changing. Anything can be here in my opinion, but someone may discuss about whether and how player can change faction