Adding further on my previous post, a Muslim brotherhood regime in Syria would force a lot of Alawite, Christian, Druze and perhaps Shia refguees into neighboring countries namely Turkey, Lebanon and Jordan. Perhaps the refugee crisis that Europe would face would be a predominately Christian, minorities of Alwaites, Druze, Shia and Sunni Muslims.
The Alwaites are going to be special targets for slaughter and ethnic cleansing, the other groups would face persecution but not the sort of treatment which would be metered out to the Alwaites. Because the Assad family are Alwaites and Alwaites formed the base support for the regime.
As I see it the Alwaites like the Alevi's came out of Twelver Shiism, however their doctrines developed in a direction that they can't really be seen as Muslims. Both don't subscribe to both the five pillars and six principles of Islam, rather I would argue they are a Post-Islamic religion like Mormonism can be see as a Post-Christian religion. The Druze religion (they don't regard themselves as Muslim) went in a similar direction to both the Alwaites and Alevi's, however they came out of Ismailism and regard one of the Fatimid caliphs Al-Hakim in very high regard. It would be kind of cool if a Timeline developed that one of these religions became a major world religion, perhaps the Ottoman dynasty adopted Alevism as their official religion instead of Sunni Islam could be a POD.