no... kabutomaru didn't kill nagato. he sacrificed some nameless-nin to cthulu-mon and then used the ninja's body as a vessel for nagato's soul. that's how Edo Tensei works.
Kabuto has some intelligence network apparently.
Now... if Kabuto went to the extent of collecting a cellular sample from nagato, then, as explained by orochimaru back when he first attacked konoha, he will be able to use the rinnegan, but considering he's been tracked this entire time by konoha i doubt he had the time.
Given the ease at which Zetsu and Tobi can move through an area, the collection of the rinnegan probably has already occured off screen.
Still, it's worth noting that "to be whole" is a bit puzzling given the context of what's been said by tobi/madara. When Tobi said he was going to use it to strengthen his eyes, i wonder if he meant he was going to cast something like a permanent Izanagi that wouldn't/couldn't destroy his eye(s). Izanagi, essentially being a genjutsu made real, could restore a person f the user desired it.