With the changes I imagine that when you start a game you will have options for both natioanality + leadership of opposing forces, therefore same nations under seperate leaders is probably possible. Aesthetically unpleasing it might be but the sides would play differently.
Of course this is all speculation as no-one knows how civIV will play but the double china scenario suggests it is possible, after all Fireaxis may want people to be able to play out a civil war scenario esp. as you can start in later ages