Kabuto is going to come back at some point. Remember Oro also has Sage mode, though not one as perfect as Kabuto got allegedly. This means Oro is going to be fighting pretty soon too.
Hashirama also has sage mode so he could fight but he seems to have his hands full with Madara.
It would make sense that some sort of power would exist that would combat the Jyuubi, as the SotSP defeated the Jyuubi using his own powers and only then became its Jinchuuriki. Obito has merely sucked up the Jyuubi.
I've got a feeling that one Naruto get the other half of the Kyuubi back then he should have a complete Yin/Yang chakra pool which would mean he has access to the same type of ninjutsu neutralizing techniques that Obito used to permanently chop off Minato's arm. It would mean that theoretically Naruto could be able to make his dad's arm reappear.
Remember though right now Obito is just fighting with his hax Bijuu powers. He still has his Sharingan and Rinnegan, meaning that even if they do start to connect with him he could phase in and out like he used to before, as well as have access to some of Pain's techniques. If he deploys these it could mean a way back in for Kakashi, as he is still out in the other dimension, to attack Obito as he phases past him.