Islamic State in Iraq existed even before the Syrian Civil War. They just took advantage of it to expand into the northern Syrian hinterlands.. Al Nusra Front is a separate indigenous Syrian Jihadist organization. I don't know if these organizations would exist in a Combat Mission SF2 aftermath, even the uncon forces are more similar to fedayeen Saddam nationalist forces rather than Religious or Sectarian organizations.
Alawites are Shia Muslims, which is why Iran supports Assad.
In real life, Syria was one of the major arteries of Jihadists to the Iraqi theater, and the Syrian government had little incentive to stop their flow into Iraq. Now that that corridor has been blocked. Where will it spread? Possibly Lebanon? Turkey's borders are quite porous and many fighters of all stripes flowed through there (Turkey missing from SF2 is a big oversight IMO. It's a NATO force and has no involvement in a full scale war right across its border?)