I believe that Nagato did not use gakidou to absorb chakra from the tailed beasts simply because it never occurred to him that he could. Let us examine three things important to this topic: Nagato's fight with Hanzo, Akatsuki's plan itself, and Edo Nagato's fighting style.
In the fight with Hanzo Nagato demonstrated no six path abilities outside of a rage influenced shinra tensei and the gedo mazou summoning. He also lost the use of his legs from saving Konan, and even IF he could use jigokudou, he has only demonstrated remote control of it, meaning that while the six paths of pain could use it, Nagato by himself cannot. From this fight Nagato had to begin relying on the six paths of pain as proxies, completely negating the NEED for himself to have a perfect body (which would still be crippled even if he absorbed chakra.)
Next, the plan of Akatsuki (under his leadership) was to collect the tailed beasts, and he would therefore be very reluctant to use any of their chakra. He was also very confident in Pain's abilities, once again presenting no need for Nagato himself to ever be in the front lines. As the leader and as Yahiko's will, it was of the utmost importance that he stayed alive (like a general in an army never being on the front lines.)
Lastly, Edo Nagato was an existence that operated very mechanically, attacking and responding to attacks in the most appropriate manner. He also did not have the six path's of pain, so he had to rely solely on his own body. With that said, the most APPROPRIATE thing to do at the time that Killer Bee attacked him was to absorb the tailed beasts chakra to reduce the potency of the attack to a survivable level, then counterattack. I am sure that if Nagato was conscious he himself would be surprised that absorbing tailed beast chakra happened to return him to his form prior to gedo mazou usage. Because he never had the idea/need to do it before being placed in a situation where he had no other choice.
What do you think?
