Hello, it is not only the base stats you have to look at but sage naruto especially. His mystery does 2 times dmg, plus repulse damage resulting in triple dmg. If it crits, it will deal even more dmg, even more so if you are lightning since wind is strong against lightning.
So indeed, no wonder he took 2/3 of your life.
base stat for elemental disadvantage is -20% which is alot. So by default wind will deal 20% more dmg in general to lightning.