In my personal opinion, I believe that they will be allowed to roam free due to Naruto's personal feelings. I think that at the end of the battle, the Kages, will agree with Naruto in not taming the tailed beasts for war usage. Seeing as the Kages are now united under one banner, the use of the beasts for war is useless. Nevertheless, the tailed beasts would have to be dealt with in order for self preservations of the Shinobi villages.
Just my thoughts, hope you guys have something to say about them.