Oh, there are good female characters - I didn't mention them because most of the ones that are really cliche are the evil ones. And I wouldn't say that they're subordinate - since the protagonist is probably the least motivated of all the characters he doesn't pull anyone, female or male, along with him. In cases where they (protagonist + one female and one male) are doing something that serves mainly the protagonist's interests, it tends to be because it also serves the interests of one of the other two (and believe me, everyone's family issues get confronted) or because they're all three of them getting dragged into something bigger. The other important good female character is definitely not subordinate to anyone.
(I like S., the protagonist's female friend. She works in a used bookstore, has father issues without being controlled by them, is sensible, and was also friends with M., the one that becomes evil.)
To some degree the morality isn't black and white - that hag is outside that binary rather than on the evil side, even though the protagonist doesn't like her. And the protagonist himself doesn't really have any especially redeeming qualities.
Dealing with being an evil little bastard - I myself am not sure, as the full reveal of what he did before losing his memory has only been outlined so far and not written. There is no moping and angsting and "you're good really" but there is a lack of explanation as to why his friends can get over his past, which I've said needs to be fixed. One of the problems, I think, is that my friend hasn't taken a clear position on how much the general public knows of the atrocities committed under the evil queen.
As for the amnesia? I don't know. The only thing I can think of is this: it was a way to create an adolescent character who is good(-ish) from the get-go but with a really evil past.