One of the big problems with calling a canon character a Mary Sue, besides all that a_t_rain and others mentioned above, is that if you define Mary Sue as partially a self-insert, how do you know that the character is one? Unless one knows the author personally, it's a mite arrogant to say, "So-and-So is Author X's self-insert."

Sometimes authors will say that they based a particular character on themselves - which JKR did with Hermione and also Harry (people overlook this latter). But otherwise, a reader can't assume that a particular character is a self-insert, unless they know the author. Unless the reader is some kind of Legilimens and can read inside the author's mind.