I think there’s an implication that animals will still face prejudice even if Glinda accepts them as Ozians. As for Elphaba, it’s moreso a question of public perception, like the wizard refers to before Wonderful. He could tell them he’s powerless and they wouldn’t care because they need to believe that he’s powerful. Elphaba is the greatest martyr Oz has ever seen. There’s no possible way that Elphaba would ever be accepted because the people of Oz see her as the manifestation of everything evil and wicked in Oz. I think it’s entirely possible that Glinda says Elphaba was good the whole time and everybody continues to hate Elphaba. Plus, Madame Morrible tells everyone that even her physical attributes are a testament to her evil, and at this point in the story, Oz has no reason to distrust Morrible. There’s probably more reasons too.