You have to realize that
a.) they were talking about malefic , evil-doing witches, not nature-worshipping pagans (although the authorities back then probably wouldn’t have drawn the distinction)
b.) There really were people practicing what we would call black magic back then. See Chadwick Hansen’s book Witchcraft in Salem, which presents the evidence. Other, more recent books cover this, too. There’s little doubt that people there and then tried to use magical means to influence the world, for good or evil, and despite the dictates of their Church.
c.) Wicca and the like are really pretty different from anything being practiced back then.
d.) Some of the authorities didn’t really believe that traditional, devil-pact witchcraft existed as anything more than a delusion, but they’d still want to hang you for even trying to hurt others, just on principle.
Salem, Massachusetts is pretty much crawling with Modern Pagans, so I can understand the desire to be witch-friendly, but it’s still way different from what they hanged people for.
Which is bad as the Olympian gods are very particular about it that kind of thing…