Black Zetsu's was obviously not meant to be Kaguya's will in the beginning. He wasn't even meant to be Madara's will in the beginning. What do you think was Zetsu's background supposed to be from his conception?
And how do you know this was not his original plan? You don't. You're assuming based on things you felt were a little off when Kishi introduced them, therefore, this thread is invalid, really. :|