[Rezz]

At this point I don't think we can assume that everything Madara is saying is going to be exactly the truth regarding the incident with itachi. The history lesson will probably be accurate, but there's bound to be some distortion via Madara trying to get things moving in a specific way to suit his own ends. That definitely seems to be par for the course with these big revelations.

Though I'm guessing that when Itachi "killed" his best friend to get his mangekyo it might have been self defense, where he will have learned of the inherent evil in the clan. Unless I'm remembering wrong, it was right before he was enlisted for a special mission for konoha. The timing would fit and would explain why Itachi was willing to wipe out his clan, code of the ninja or not.