No, I’m pretty sure his “not you” is almost entirely literal; you seem to be missing the analogy. In the hypothetical he’s considering (“suppose that boy had helped you”), the situation of the boy with respect to her is analogous to the real situation of her with respect to Snape. Hence when he points out that she would probably consider him bothersome… well, you see. “Not you!” indicates that, though the analogy is present, that wasn’t what he was going for; he is simply considering a hypothetical about an actual boy, not making a jab at her by means of analogy.
(Or in short, JoshuaZ is right. Added: See also jaimeastorga2000′s comment.)
No, I’m pretty sure his “not you” is almost entirely literal; you seem to be missing the analogy. In the hypothetical he’s considering (“suppose that boy had helped you”), the situation of the boy with respect to her is analogous to the real situation of her with respect to Snape. Hence when he points out that she would probably consider him bothersome… well, you see. “Not you!” indicates that, though the analogy is present, that wasn’t what he was going for; he is simply considering a hypothetical about an actual boy, not making a jab at her by means of analogy.
(Or in short, JoshuaZ is right. Added: See also jaimeastorga2000′s comment.)