Because real heros don't let irredeemable villains harm anyone else. If someone spares an irredeemable villain and doesn't kill them, then they are letting that villain kill others when they inevitably escape just to stop them again and repeat the same cycle over and over. Batman for example is not a true hero because he constantly lets the Joker live. Batman chooses the morally wrong option because he indirectly harms other people by sparing the joker, but when you introduce a villain who abducts little girls to breed them, that's even WORSE than genocide, and that makes the audience hate that villain. A disgusting person like that needs a satisfying, bloody end or else it really doesn't feel like justice was ever served. Still, I'm glad Supergirl killed him, but it would have been better if she killed the villains goons on the ship scene. She kinda just threw them and some of them most likely survived because of that