The man that knows the truth about Itachi was his former lover, his best friend. His best friend came out of the closet dragging Itachi with him. Itachi didn't want this information to come out. Things spread quickly through the Uchiha clan and he had to kill them all and his best friend before he got through the village.
He spared his younger brothers life at that time, but when he saw him years later that he was getting close to another boy (Naruto) he told him he had to kill him to protect Sasuke from the same fate