The witch burning reference you refer to is on page 14 of the book Mere Christianity.
First off at this point C.S Lewis is not even close to getting into Christianity, this comes much later in the book. So Christianity has no bearing on this section of the book, as he is trying to establish the fact that humans have some sort of moral code/or scale by which we measure right and wrong. A scale that is similar to all humans.
Someone Lewis talked to had tried to use the argument that morals had changed because 300 years ago people in England were burning witches.
Now Lewis is not condoning the burning of witches, rather trying to explain how if we lived in that period of time, believing that there were witches. People who sold themselves to the devil for supernatural powers, which they used to kill their neighbours, drive them mad and bring bad weather. That we would probably agree that if anyone deserved the death penalty then these people did.
Because we have advanced in knowledge, no longer believing in witches there is no moral advance in not executing witches when you do not think they are there.
Lewis also says "You would not call a man humane for ceasing to set mousetraps if he did so because he believed there were no mice in the house."
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Saved by an incredible Grace.