Though the Rinnegan is the ultimate exception in the ninja world. I don't see any village, particularly at that time, who would want to pass on the chance of having a shinobi with the rinnegan.

It is curious to think what Obito would do in this situation, manipulating Nagato would be more difficult.

If he did have to kill nagato though, I don't think it would be difficult for him.

Visual Genjutsu does not work against the Rinnegan and Nagato is the opposite of stupid. He would figure out Obito's intangibility just like Foo, Torune, Minato, Kakashi, and Madara did. Obito's only chance is to warp him into Kamui's dimension but considering Nagato's speed and versatility along with his techs at his disposal, he only needs to touch Obito one time to initiate ripping his soul out and once that starts turning intangible won't save Obito. Not to mention whatever chakra based tech Obito uses will be absorbed, and if Nagato physically touches him he could absorb Obito's chakra that way too. Obito's only chance is warping Nagato away.

He needs to touch obito with his hand to start yanking out his soul and we don't even know that he knew how to do that without obito teaching him. Obito just needs to touch nagato on a part of his body that's not his hands and obito presumably has full intel on rinnegan abilities. Nagato doesn't have any good counters to obito's intangibility except ''maybe'' the deva path but obito might know about the time between deva path attacks if BZ told him about it.

Obito tought him how to use the Rinnegan?

the wiki said obito offered to show nagato how to unlock the full potential of his rinnegan but I checked the chapter in the citation and it doesn't explicitly say that ''but'' it does say that nagato hadn't unlocked the full potential of his rinnegan yet meaning probably either obito helped him do that or he did it on his own but either way it makes no difference to the point I was making.

Nagato was slowly figuring out the Rinnegans 7 Path abilities on his own. The only ones he didn't were the ones he didn't use in the series that were particular to those eyes which were Tengai Shinsei and Limbo.. because he wasn't told about them.. because Madara didn't tell Obito about them(Madara isn't stupid, he kept his best techs a secret from even Obito)

As someone said, they probably wouldn't have accepted. They wanted to save the Hidden Rain from Hanzou. I think though it would've been a much better story if he had, though. If they'd have come to Konoha and been revealed to have ended up with Root, there are so many possibilities.

Intriguing thought, Danzo may have even tried to steal the Rinnegan. Or make Nagato one of his loyal followers.

Yeah. Danzou should've been a much bigger threat than he turned out to be.