Technically, being pardoned means "you did the crime but we are going to let you off". For example, Alan Turing was guilty of breaking the law as it existed at the time. He was posthumously pardoned because the government of the time thought the optics would be good we recognise that the law was unjust and the punishment inhuman.
I haven't read the whole article but it seems to me that, in the main, the women who were convicted of witchcraft usually had confessions extracted from them by means of torture. They should not be pardoned: they should have their convictions quashed.