Even if sasuke is in the EXACT same situation as naruto meaning
.pein blew up Konoha and fought various jonin level ninja (therefore not full chakra)
.Nagato isn't what you'd call "healthy as a horse"
.Sasuke havings slugs and intel
.deva path not able to use its abilities for a little while
.Sasuke's at full chakra
.peins trying to capture Sasuke
....then sasuke can't just turn into a mini kyuubi whenever he's in a little trouble, he can't make use of the shadow clone jutsu to take advantage of the 5 sec gap, he can't spam summons close to the level of naruto, and he doesn't have the SM strength to just hulk smash them,( although he does have a severe speed advantage over naruto in SM form) pein would most likely win.
If this fight ever somehow happend without plot no jutsu to get in the way I would literally bet money pein would win, because even if sasuke DID beat all the peins (not probable)
then how would he track Nagato? Then if he did I couldn't see him use talk no jutsu (imagine that

) on Nagato to save his butt
overall I think that SOME of the people who are for pein (right choice in my opinion) are underrating sasuke on how long/bad sasuke would lose/last.
but MOST people who are for sasuke are overrating him AND underrating pein.