It shouldn't. When Jiraiya used genjutsu on Pain, it only affected the bodies he actually used it on. If Sasuke were to trap all of them in a genjutsu, then it would work. However, I'm pretty sure the Rinnegan is supposed to be able to see through most genjutsu...My question is, would sasukes genjutsu engulf all six pains if he were to get one of them?