Well you're not kill them, but you're leaving them fainted and injured in the wild, so it's never 100% clear what happens to them, if we assume pokemon don't eat other pokemon or that smaller pokemon stay away from predators that can eat them, they're probably fine and wake up later.
Well.... them being unconcious probably leads to them getting eaten by other pokemon......... ..... ........ :D
THE HORDES OF PSYDUCKS I'VE BEEN SEEING
GOOD GOD WHAT HAVE I DONE
Well think about it pokemon know they faint right, and you see balanced pokemon in the same area it's likely pokemon stay near pokemon that can't or won't eat them so it's probably fine, you're not a mass murderer, probably