It's fairly obvious from her painting that her recognizing him on sight is the most likely. He was clean-shaven in the painting, and would have had a beard in any literature from the era if he had been a practicing Sikh.Yes, but there's absolutely nothing about Khan's clean-shaven, relatively short-haired, turban-less appearance that would give her any reason to suspect he was a Sikh, so the scene makes no sense.
Unless we assume that she recognized him as Khan Noonien Singh on sight but chose to keep the knowledge to herself, because she wanted to hoard the historic discovery to herself or something.