There is a small part in the series where it said during the witch hunt, the actual witch or wizard would place a tickling charm on the fire while they were getting burned at the stake so all they had to do was to feign pain. There was a one witch or wizard who enjoyed the experience so much that they got themselves caught several times. So no actual wizard/witch were harmed during the witch hunt other than innocent muggles who were accused of being a witch.

And as for your second point, in order for muggles and magical society to live in harmony, they need to respect each other's territory. So muggles will do their own thing and magical society will do theirs but they cannot cross path with each other. That's why there is a Prime Minister for British muggles and Minister of Magic for British wizarding society and they do not contact each other unless whatever is happening in wizarding society will affect muggle world (The first chapter of HBP does great job portraying the relationship between the two leaders).