Well, given all of the things that SHIELD knows about, it wouldn't stun me if they knew about sorcerers. Also, there would be no reason to target Strange before he was sorcerer - he'd be someone Hydra wouldn't really have a problem with. It wasn't like he was especially influential or even liked by... literally anyone.
So, timeline incongruity aside, you'd kind of have to assume that he was, in fact, magical when they targeted him.