Are there sectarian elements in the Syrian opposition? Certainly. Does this mean Syria's minorities are at risk if Assad goes? Certainly not. In fact sectarian tension is precisely what Assad relies upon to stay in power, and the useful idiots who think this is a Sunni uprising against an Alawite president fall right into Assad's hands when they chant sectarian slogans. Of course this is nowhere near as widespread or as pervasive as Arab anti-imperialists would have the world believe. The real risk is that Assad's repression will continue to marginalise more moderate elements of the Syrian opposition, drowning out their voices the more urgent the calls for revenge become. Naturally all he has to do is continue turning the tap of violence looser and looser until he blackmails the Syrian people into accepting him as the sole alternative to complete chaos.
There were minorities in Syria before Assad and there will be minorities in Syria long after he is gone.