It seemed like I was supposed to relate to the protagonist somehow, but I just really didn't. She was a psychopath through and through. Her sister wasn't likable either, but she was the lesser of two evils.
I can't claim to be able to see inside Nancy Kress's brain, but my impression was that the reader wasn't meant to identify with either character, except maybe in a purely intellectual way: you're supposed to understand why Karen has come to be so heartless toward her sister, but you're not supposed to agree with her actions. It's a character-based piece, but neither character is meant to be sympathetic.
But that's just what I took from the story -- I didn't get all that from inscribed stone tablets that Kress herself left by my door.