Even so, popular media paints a different picture of the witch. Yes, you have the wicked witch of the west, but also the good witch of the north. There is a comic I recall a while ago called W.I.T.C.H which was about 5 teenage girls with magical powers, defenders rather than the cackling evil witch. Sabrina has good representations of witches (both series do though one is definitely darker in tone). Bewitched had good witches, diskworld has granny weatherwax and his dark materials has some incredibly awesome witches and lets not forget the witches in Harry Potter. There might very well be complaints about the term witch and if WotC were going to create a witch class/subclass it might be enough for them to use a different name but I think in general those complaints are going to to get drowned out by all the popular media which have witches in them.Where I think "witch" differs from those other names is that it was a label used in the cause of torturing and killing people, usually women, and as such it is still used today as a pejorative for a woman who, well, doesn't conform to behaviors some men prefer. Upthread I linked to an example where feminists have (somewhat humorously) tried to re-claim the word, but in my mind that just emphasizes its loaded meaning.
So it's not that "witch" has historical meaning that we might get wrong, thereby offending people who follow certain religions, but that "witch" is specifically a word used for oppression, not just in history, or even in near memory, but in the present day.
I'll leave you with this, which I find quite funny and yet it illustrates the negative connotations of the word: