Before I begin, I would like to point out 1 thing: this is mainly speculative and for fun - I may be wrong about several points and others could be irrelevant. ========================================================================= Now first I would like to recall some history/facts in the Naruto-verse that has been established or can be derived from being caught up in the manga:
* The Rinnegan is originally the bloodline technique of the Sage of Six Paths and is the final evolution of the Sharingan only to those who wield Senju DNA as well as the Eternal Mangekyou Sharingan.
* The first Hokage's bloodline technique is much more complicated than simply Mokuton (wood-style), and more broadly, it is capable of influencing life forces; his cells are shown to be capable of creating life (Zetsu), maintaining life (Madara), suppressing life (Kyuubi), or enhancing life (Obito & Madara).
* Nagato's capacity to wield the Rinnegan is still somewhat of a mystery. We know that the Uzumaki clan is distantly related to the Senju clan, and we know that the first Hokage married Mito Uzumaki thus giving members of HIS lineage both clan's lineage, but why does Nagato have ancestry who belong to both clans if he wasn't born in Konoha?
* The Uzumaki clan wields the most powerful of the sealing technique(s) known to the ninja world; they are also the most adept Jinchuuriki and are now a lost clan - do note that every single Jinchuriiki of the Kyuubi has been an Uzumaki so far.
* A peculiarity arises when one examines that the Uzumaki clan's shrine is for some reason on the outskirts of Konoha, which may note a somewhat strained relationship with the village similar the to Uchihas (or maybe it was to protect their secrets). Also note that their masks are protected by a black flame. =========================================================================
========================================================================= To be honest, I don't think that the mother we saw Nagato with as a child was his biological mother - the Uzumaki clan was supposedly a clan whose members naturally had immense amounts of chakra, however his mother seemed extremely easy to kill by two ninja who couldn't take a child(Rinnegan or not). It also doesn't account for the fact that he had Hashirama's cells as well. I believe that there was some reason or another Nagato had to remain a mystery, and thus removed from Konoha.
I think that the ones who sealed the Uchiha clan's love were indeed the Uzumaki clan as they were the only ones with a sealing jutsu powerful enough. I'm tempted to say that they also sealed the Amaterasu inside the Sharingan given the black flames protecting their shrine and how oddly Amaterasu stands out from the rest of the Mangekyou Sharingan abilities shown thus far, as well as its unique strain on the body (bleeding eyes); Sasuke has shown that this side-effect still occurs even after the user has the eternal Mangekyou Sharingan. =========================================================================