I think the biggest surprise is that she held on to her individuality in this path long enough to expire as a human when she broke down so much worse in the judgement route that Black Alice dusted her before she could become a problem and even when they go to retrieve her with Luka not understanding entirely yet she still asserts her will to kamikaze Chaos Goddess Black Alice from bothering Luka anymore on that path.

That being said, does Sonya remember the other routes and their endings too because of what she really is or does only Luka and everyone he shared his eye power with in that one scene?