There will be plenty of battle skirmishes, raids, rescue attempts, etc. for opposing factions to meet and interact. They might also stumble upon each other while roaming around the countryside. Only the comm channel will be kept separate, the logs community will be shared by both.

But yes, there has to be OOC permission for battle consequences, no one will have to play out something they don't want. (Working on the FAQ right now.)

I might put up a sort of 'neutral ground' between the two factions, so either side can have CR without having to fight each other immediately.