Yeah, but, what sort of agreement? You just said the kyuubi would not come to terms...I already have your eyes brother...
I think that yes it will be an internal fight as well ... However on top of all that I believe that they may come to an agreement .. perhaps Naruto mentions Madara .. I doubt the Kyuubi would want to be under someone elses will .. Especially Naruto's .. therefore I think an 'agreement' will be made. There will be quite the struggle before this however.