Well that's where Scalia's statement comes in - he argues that the state has no duty to avoid executing innocent people, only that all relevant procedures were followed. To use an example from history, if witchcraft was a crime, and the townspeople found someone guilty of witchcraft, they have no duty to accept a time traveller's defense that witchcraft is scientifically impossible and the person is therefore innocent. The "due process" was the trial and witch tests, not a modern scientific consideration of the facts. I don't know Scalia's actual opinion, but I would be surprised if he did not find these witch executions judicially justifiable. Presumably he would argue that the proper way to avoid burning witches at the stake would be to change the laws supporting such activities.