If you will have a look in Google Earth at the area where that supposed Syrian reactor was located, you will find no single sign of any SAM system in the entire area. No active site (you may use the historical imagery feature), no abandoned site - nothing. The nearest SAM is located 40 km away near town of Deyr Az Zawr, and its effective range is 25 km. So what are you talking about?

For me, it appears that either Syrians relied on secrecy rather than any defences, knowing that they will attract unnecessary attention placing SAM batteries there, or, more plausible, the object in question had no relation to any nuclear program at all. If they would really want to protect it with air defences, they would built it in the areas of the country already filled with SAM sites, and not somewhere in the outback, close to Turkish/Iraqi borders.