He used chidori because it was the only technique ment for piercing and the strongest jutsu he knew, not because it's lightning nature has an advantage over earth.
Kishi made a mistake with that nature chakra thing. Now that it's been introduced way too many people think that decides the winner. It doesn't. The stronger jutsu will win most of the time.
"For Feanor was made the mightiest in all parts of body and mind, in valour, in endurance, in beauty, in understanding, in skill, in strength and subtlety alike, of all the Children of Illuvatar, and a bright flame was in him"