Madara would destroy Nagato even without the Rinnegan. He possesses the Eternal Mangekyō Sharingan, that's enough to defeat Nagato. Already the Mangekyō Sharingan is overwhelming. It gives you powerful Genjutsus - strong enough to control even the Kyuubi, also Amaterasu, which will hit Nagato in any case, because it arises directly in front of his body, and on top Susanoo, the perfect attack with the perfect defense. The Eternal Mangekyō Sharingan is the higher stage of the Mangekyō Sharingan and gives you according to Itachi true power. With this unstoppable power, Madara took control over every shinobi clan the Uchiha encountered (Stated by Itachi, chapter 386, page 10). Also Tsunade said, that Madara is more than a man, she said that Madara is an ideal, the name itself is power. Madaras hype is 100 times bigger than Hashiramas, we don't know whether Hashirama defeated Madara in a 1on1 battle, all we know is, that Madara was known as a true legend, an invincible and immortal ninja and the strongest Uchiha ever. Even without the Rinnegan, Madara would defeat Nagato in any case. EMS Madara will defeat Nagato, EMS Madara with Senju Hashiramas genes and the wood release will destroy Nagato, EMS Madara with Senju Hashiramas genes and the wood release and also the Rinnegan will destroy Nagato in any case. Itachi with his MS ist about Nagatos level, they're both playing in the same league, that's fact. It should be clear, that an EMS user like Madara would defeat Nagato. In the case that Itachi would obtain the Eternal Mangekyō Sharingan, he would be obviously on a higher level than Nagato. And the current Madara, which possesses the EMS, Rinnegan and the wood release and is Kabutos trump card, could not defeat Nagato?
End this discussion, Madara is stronger than Nagato.