Taking into account most reckonings and analysis I've seen, it seems pretty safe to bet that whether or not Syria remains a unitary state, there will be a long-term struggle for power between hard-core Sunni Islamists and other groups in this predominantly Sunni Muslim country who prefer a future political system (a) infused with, but not dominated by, principles enshrined in sharia and (b) incorporating elements of liberal-secular nationalism. Whatever one's take on Baathism specifically, the fact of the matter is that late 19th- and early 20th-century Syria was one of the hearths of secular Arab nationalism.
A report in today's NY Times limns the shape and dynamic of local political tensions that may dominate Syria's political life: hard-core jihadists (specifically, members of the Jabhat al-Nusrah) asserting their preference for strict adherence to what they view as properly Muslim conducr, versus local community members intent on determining the shape of local governance without jihadist interference. The report makes very clear the potential for violent confrontation.
Some of this puts me in mind of the situation in Iraq after the US invasion in 2003. Al-Qaeda-type jihadists entered Sunni areas and were able to dominate local communties because they were well equipped and well organized. But in enforcing their strict moral and legal codes they also resorted to such brutality that the locals turned against them, with many of the locals later joining the Sunni sahwa ("awakening") militias that played such a huge part in ousting al-Qaeda (at least temporarily) and dampening down the general level of violence. (That's the same dampening of violence that John McCain and his ilk insisted on crediting to the Petraeus "Surge" - which is the basis on which McCain speaks of Iraq as a US "victory.")
Of course, the Iraq situation was very different from that in Syria because the catalyst for so much of the violence there was the invasion and occupation by the US. To be sure, the Nusra jihadists and others are serving as proxies for the Saudis and other hyper-Sunni regional players. But my real point here is that as the writ of the Assad government in Damascus continues to shrink, and the rebel groups continue to be unable to come together to fashion a more centralized political solution, Syrian communities will be having to take matters into their own hands, on the micro-level. The potential for conflict is obvious.
And what kind of "Syria" emerges from all of this is anybody's guess