To get the Excellent score on "Leaf Village Destruction" mission, use Itachi as your character, then select Kakashi's Lightning Blade as one of the jutsu. Then follow these steps.

1. Use Tsukuyomi to get Orochimaru to half of his original health. [If you are close or a little past it, then that works too.]
2a. Use Kakashi's Lightning Blade to get Orochimaru to lower his hit points drastically. [It gets stronger as the power meter increases.]
2b. If Orochimaru's hit points aren't low enough [below 80%], then use Amaterasu once on him.
3. Get close to Orochimaru and use the Third Hokage's Admantine Nyoi on him to complete the mission.

If that was your last mission, then congratulations! You beat the game! :D