Boy does this take me back.
I honestly don't see why it has to be rape or anything similar to that. Madara has been shown to dabble heavily in cloning research (Hashirama and Zetsu). Also the prerequisites for being able to even possess Dojutsu and use it without fatigue was never fully explained it was only mentioned that Hashirama could. Like how Danzou used many sharingan's without massive chakra drain by transplanting his cells.
I doubt that a normal Uzumaki could simply use the Rinnegan as Nagato was able to without without fatiguing himself because if simply being from the Uzumaki/Senju clan could allow you to be able to use them even more efficiently than even the Uchiha could why didn't the Senju clan simply take the eyes of each Uchiha they killed for their own they could have easily killed them with their own weapons, or why didn't Orochimaru take sharingan and implant them in an Uzumaki and steal his body instead yet he insisted that he needed an Uchiha.
I think that it's possible that the Rinnegan are in a level of their own after all even Madara needed Hashirama's cells to even acquire it. I think that it may need both halves of the puzzle (Senju & Uchiha) to even work correctly I think its possible that using them might have even caused Hashirama some degree of strain after all even with his almighty cells he is still only one half of the six paths.
Nagato was special somehow whether it be that he was simply infused with Hashirama cells (seems a bit redundant on an Uzumaki) or is a Madara/Uzumaki clone created by the combination of his DNA with some Unknown Uzumaki.
On a side note I find it a bit funny that people were willing to look at how Minato/Naruto & Obito/Zetsu looked similar yet simply dismiss Nagato/Madara relation outright saying that Kishi's art style isn't that varied.