No. Pein is most likely the anti-villain.
I don't think so.
When Pein overthrew Hanzou by killing him, he also killed everyone related to him even if they were innocent. Is that noble?
Pein is the leader of a group of criminals. It doesn't matter that he didn't establish the organization. I doubt he's leading it against his will, and I'm sure he knows all about Itachi's, Kisame's, Sasori's, etc., colorful pasts.
He seals Jinchuuriki, killing them in the process.
He wants to acheive peace, which is noble, but his methods are very very twisted. He wants to do it through war, fear, and suffering, by making people feel the pain he did as a child. Anyone sane knows that's not noble.
If anything, he's a horrible perversion of an anti-hero with a misguided goal. So basically, he's a crazy villain.
Itachi is the same as haku and kimimaro in terms of "viallain"
...wait, how?
Itachi isn't doing what he's doing out of love and loyalty for someone else.
He's doing everything for himself and to ascend to new levels of power, unless miracolously proven otherwise.