@Tersione
I'm not saying I dislike the ending myself, but I did kinda feel like the doctor's feelings could have been explored in more depth. There was the one page where she apologizes, and it's enough to satisfy the narrative, but I feel like another page or two exploring how the doctor really feels deep down would have given her change of heart more weight. (Not that I'm meaning to criticize the story, it's just that it might be why people don't quite empathize with the doctor and might have thought she deserved the bad end.)
@Aoitenshi
Although I don't think it would work as a series, it does seem like they didn't get much time to dig very far past superficial feelings. Perhaps a two parter might have been enough?
I suppose you could still have sort of a happy ending if the birdy died, then the doctor died and they both got reincarnated as birds. (And then the people in the town would have realized their mistake for being so mean, once they lost their doctor.)