It seems to me that Itachi is not actually a villain, but instead was forced to do the evil things he did.
When he came to capture Naruto initially, he told Kurenai and Asuma that he did not intend to hurt them and it seems like he had chances to kill them (Kurenai Asuma Kakashi) but did not deliver fatal blows, instead just tried to stop them.
For some reason, i think Itachi used Mangekyou Sharingan on Kakashi so that Kakashi could copy the technique/ learn how it works, and use it himself for good. By good i mean that Itachi probably has similar motives to the Konoha ninja, but is in a complicated situation.
The situation being Tobi's control over Akatsuki / Itachi. Someone mentioned on the boards that they thought Tobi actually is the one who made Itachi wipe out his clan. And Itachi probably was not supposed to leave Sasuke alive, but did because he is not a villain, and needed someone to surpass him and eliminate Tobi.
And then, Kisame says "From here, it looks like you are crying, Itachi" He seems good.