So far at least.
We have a cold war going on between Freeport and Qeynos at the moment, but it could heat up and things could change. I don't see them adding the level of Faction PvP WoW has, but it could look a lot like WoW PvE servers. (no grouping, no talking, KOS to the other side's guards, etc.) Maybe grouping with the other side too much could result in losing your citizenship, and having to do something like the defection quest to get it back, or become a citizen of another neutral third party city like Maj'Dul.
They have room to add interesting stuff like that. I think it would be fun.