It might not have come out then because he wasn't in much emotional stress at the moment. and we still don't know if sage mode and kyuubi fusion works or not because remember it disrupts naruto's chakra
I think he'll figure out a way to balance it. First he balanced physical and spiritual energy. Then he balanced shape manipulation and wind nature. Then he balanced physical, spiritual, and natural energy. I'm pretty sure he'd be able to master balancing physical, spiritual, natural, and kyuubi energy to become insanely strong.
Or maybe it's like this: since kyuubi chakra is still just chakra (albeit more sinister), he could increase his amount of chakra so that when he balances the chakra with the natural energy, he would have to take in a crap load more natural energy to enter sage mode. Fukasaku showed the diagram of how the 3 energies (physical, spiritual, natural) have to be perfectly balanced. So the amount of natural energy one can take in and balance is directly proportional to the amount of chakra that person has. So when Naruto pulls out some Kyuubi chakra, his amount is skyrocketted and he'd be able to take in much more natural energy and sustain Sage mode indefinitely.
For those who still don't get it,
To enter sage mode you need 3 equal parts to make a whole so 3/3
physical 1/3 or ~33.3%
spiritual 1/3 or ~33.3%
natural 1/3 or ~33.3%
Since phys and spirit energies together make chakra,
chakra 2/3 or ~66.6%
natural 1/3 or ~33.3%
Let's say Naruto's sage mode is 150 units
100 units chakra (~66.6% of 150)
50 units natural (~33.3% of 150)
If Naruto pulls out 100 units of kyuubi chakra making total chakra 200, he would need to bring in 100 units of narutal energy to balance it in Sage mode
200 units chakra
100 units natural
Giving him 300 units of energy total doubling the length of his Sage mode.
That's what I'm thinking.