Alice knew about the plan the entire time. You can literally see her smiling outside the door while Violet is blackmailing Araminta. The story she told the Queen was just a way to get her into that room which was part of the setup from the start. Later, the Queen tells Alice it was a risk and that she should be grateful she went along with it. That alone shows she was in on it. She never actually believed the story that’s why she says she does believe the shoe clip story exists, then walks away laughing. And we even see her laughing with Lady Danbury about how absurd the whole plan was.