It actually makes a great deal of sense, as well... the Western Shift from Tribal to National thinking didn't happen overnight, either, and if the reality is that it NEVER really happened here, then it's hard to imagine how to end the struggle.
Ultimately, in the West, the struggle ended when the biggest and baddest tribes were able to keep others in line until the nation replaced the tribe culturally (often through a kind of cultural genocide we simply wouldn't allow today) or by completely removing people from tribal homelands through colonialism. And even then, the hold to nationalism is always tenuous at best... just look at the disaster that was Czechoslovakia.
If anything, the Sunni-Shia division adds another, third force competing for the identity of the people, one capable of replacing tribalism but still not entirely compatible with nationalism.
Short Version, if this is right, these people will never be a Western Style nation. The road there is one we don't let leaders take anymore, and for good reasons. Our peacemaking might be exactly the thing preventing real nationalism from forming.
My head hurts.