Interesting theory, but didn't Gosho mention in an interview that only the Boss's name appeared in the manga, not the actual character? If Agasa were really housing Haibara to make an antidote for Mitsuhiko, why would the Boss send his agents to track down and kill Sherry? Plus, Agasa knows Conan's secret, so I'm surprised Conan hasn't been killed yet if Agasa were really a high-ranking member of the BO.
Out of curiosity, has anyone tried making a list of all the names that appeared in the files released before Gosho's interview on the Boss's name?