It means that though the Witch knew the Deep Magic, there is a magic deeper still that she did not know. Her knowledge goes back only to the dawn of Time. But if she could have looked a little further back, into the stillness and darkness before Time began, she would have read there a different incantation. She would have known that when a willing victim who had committed no treachery was killed in a traitor's stead, the Table would crack and death itself would work backwards.