I was playing naruto shippuuden ultimate 4, and defeated itachi as in the anime, and noticed the smile on his when he was hit by narutos rasengan.

later in the manga you learn that itachi was really a great guy ;D and when he talked to naruto he showed that he cared for both sasuke and konoha.

When he saw how much stronger naruto had gotten, he understood that naruto would be able to bring sasuke back sometime and that konoha had someone that could protect it, thats why he smiled, he was satisfied.

Thats what i think :D