I can see the Kyuubi helping Naruto. Specifically I think it may act as the gatherer for Naruto, eventually allowing Naruto permanent sage mode. The reason for it wanting to help Naruto now is that it knows Madara will make it his bitch given the chance. The Kyuubi has no way to fight Madara directly. Helping Naruto may be its best method to secure eventual freedom.

By eventual freedom I mean NOT being combined into the 10-Tails and, perhaps, being freed as Naruto dies or hoping that the next container screws up. Helping Naruto, there is some hope for the Kyuubi.