I think if Ilya had been awake, I think she would have killed him immediately. Since he was asleep, I interpret that scene in a couple of ways: she was standing there wondering if she should kill him, but she was also in a bit of shock and regret because she knew how traumatic it was going to be for the child when he woke up. Even at her most extreme, I don't think that Elizabeth would want to cause this sort of visceral trauma to a child if she could avoid it.