The stat.damageDealt doesn't take any damage reduction like armor, protection or resistance into account when incrementing the score.

Example: Summon a Zombie with resistance 5 which makes it invulnerable. Hitting the zombie will still increment the stat.damageDealt score as if the resistance effect wasn't there. The same behavior is seen with armor, and armor with protection enchantments.

This also applies to stat.damageTaken.
As of 14w31a. stat.damageTaken is tracked correctly.