Remember when Naruto was stomping Madara after the Gai fight? With both seals he would have ended it right then and there.
Sasuke is the last descendent of Indra. If he died then the cycle ends.
Again, it's a mere assumption that Naruto with both seals > Naruto and Sasuke working together. You can't say that because Naruto with both seals doesn't exist.
I know we're speaking theoretically here. Maybe Naruto would be able to defeat Madara before he got his second Rinnegan. But what I'm saying is that it is highly unlikely that Naruto with both seals would be stronger than the two of them working together. Even if the parts would be the same (which it really wouldn't, seeing as Naruto would not have had the Rinnegan) teamwork > solo attack.
Also. Indra's reincarnations have died before. Indra doesn't die with his reincarnations. If Sasuke died he would reincarnate into another person.