How can a word that was created as an excuse to kill people be use as a historical category?

the word pagan meant peasant and still does in some of europe but in the 1300 there was a group of people the were burned at the stake the christians at that time created the new pagan as a derogatory term or slur word to justify killing them and know people label religions under this catagory when in fact its like history teaching the n word for blacks