The original version of "Shout at the Devil" was called "Shout with the Devil" and instead of beginning with "He's the wolf crying lonely in the night, he's the blood stain on the sta-a-a-age" it began with "I'm the wolf crying lonely in the night, I'm the blood stain on the sta-a-age."
The original version of "The Drugs Dont' Work" has the lyric "They just make you worse, but I, know I'll see your face again" though the original went "The drugs don't work, they just make me worse, but I, know I'll see your face again."
Works change and evolve. I can't speak to the fact that it was published over her wishes, but I think that's just people mythologizing Lee because she's still alive. If an unpublished Hemingway book surfaced, would we be having this discussion? I doubt it. Watchman is a piece of literary history and should be released.
Also, I haven't read very much about this apart from the Gawker-style headlines of "You'll Never Guess How Atticus Finch Became a Racist Because Oh My God!!!!!" but I'd like to think that in Mockingbird, Scout visualizes her father as a heroically honorable god among men in the same way children do with their parents, like my own for example. Later, as an adult however, she realizes the reality is that all men are flawed, especially her father who can now be seen as the racist he always was.