Sometimes they kill brothers or grandmothers instead. Or fathers, as was mentioned already with Mufasa.
They haven't always killed family members of the hero. Zootopia didn't, and neither did Sleeping Beauty, Hercules, Tangled (unless you count Gothel who was also the villain and not Rapunzel's real mother), or Wreck-It Ralph (though they did program a supporting character with a backstory of her fiance being eaten). I haven't seen it in a while but I don't think Peter Pan did either. I'd say Mulan, except maybe it counts that Shang's father was killed. But, most of them did, either by having some dead by the beginning, or killing them either onscreen or offscreen in the course of the story.
I still think that, between villains and family members of the hero, they stopped killing the wrong one.