Then explain how Naruto, even when having control of Kurama Chakra, couldn't even transform into Kyuubi Chakra mode without Kurama's cooperation? Having the Bijuu's cooperation is an enormous powerup! Instead of him draining your Chakra while you use his, he instead adds to your Chakra, to bring one example of a direct benefit of a Bijuu's cooperation. Besides, the Sanbi was probably much like Kurama at the time, not really giving a damn as long as he got to smash shit up(and consequently come one step closer to freedom in his mind), thus not really giving a damn if Yagura(by all rights, just another person stealing his power and imprisoning him) got controlled by another *******.