Genjutsu really isn't that big of a deal especially in Peins case. I don't know why anyone thinks Itachi would be able to kill Pein yes Itachi is a master of genjutsu but his normal genjutsu would be easy enough to overcome and we don't know enough about MS to know how it would work.

Anyway I doubt we will ever see a Pein vs Itachi battle because for one thing the closest we have ever come to seeing two different Kekkei Genkais face off against each other was Sasuke vs Haku. Itachi doesn't have any reason to fight Pein and even if they do face off I would give Pein a tremendous advantage because not only were Itachi and Kisame intimidated by Jiraiya but Pein is the leader of akatsuki so rinnegan or not its safe to say that he is just plain stronger than any of the other members.

Since he is the one who formed the group he must know all the members and their strengths and weaknesses and since he is partners with Tobi I would think he knows all about the Sharingan and its abilities and exactly how to defeat it. Not to mention that it would be six on one and we have yet to see Itachi use MS on a non sharingan user or use genjutsu on multiple opponents at that.

Itachi's strongest justsu or doujutsu's which are easy enough to avoid and even if he does catch Pein in one, he should be strong enough to be able to break out. Even if the jutsu is inescapable like Jiraiya's was Pein has other bodies. I doubt Itachi would use genjutsu against Pein anyway because someone like him should have tremendous mental fortitude.

Anyway this post is getting lengthy and we don't know much about Itachi since we have yet to see him in a serious battle, and I'm sure we have seen very little of what Pein is capable of so having this discussion now doesn't make sense.