Pure is a word used in both positive and negative contexts. When used in a strictly scientific sense it's fine just to indicate the lack of contaminants in a given substance, and quite often this is needed to be able to create certain chemical compounds or alloys.
It all goes awry when humans start considering themselves more pure than other humans or even animals and robots. We've seen it in World War II where the leaders of the German people wiped out millions of other humans simply because they were deemed 'not pure'. And even today there are people who think themselves better than people of other races, or other people who have a different view of reality than they do.