I am actually thinking that the fruit warped her mind, she was/is not "evil". It's kind of like with Madara's Rinnegan in Nagato, it eventually corrupted him after enough use. For example, when he used the Rinnegan a lot to fight off Hanzo after Yahiko died Nagato got the "evil" smirk, he lost his mind to it like how Obito said he almost lost it. The same could be said for Kaguya, after she ate the fruit of the tree, after enough use of the power the Juubi "warped" her mind and she "lost" it to the power of the fruit. That's what I think anyway. Your thoughts?