Well we haven't seen the full capabilities of his Gunbai yet, nor has it even been discussed at any length at all during the manga, so making assumptions about it's capabilities would be dumb.
On that note, it did redirect a mini-bijuudama, so I don't see why not.
i doubt his fan can deflect a big bijuu dama. he would probably just tank it with susano. madara will obviously have a counter for bijuu dama in the next chapter.