Pain beat Sage mode Naruto too, but yea Sage Mode > 2nd Stage Curse Mark.So Sage Mode Naruto>2nd Stage Curse Mark Post Time Skip Sasuke? I don't disagree just curious.
If you take 2nd stage Curse mark as giving the same kind of multiplier as the V1 One-tail Kyubi cloak (From the Valley of the end fight), then since Sage Mode Naruto can take a 4 Tail V2 Kyuubi Cloak in sheer power Sage Mode wins. Besides, there literally was nothing Sasuke could've done to Nagato since he didn't even have the Mangekyou Sharingan at the time.