The "turba" choruses in Bach's St. John Passion are some of the catchiest and fun to sing - and I think that's exactly what Bach intended. Going along with the mob and being swept up by their energy is easy and fun, until you (hopefully) realize you're calling for someone's death...
AND the anti-semitism in the St. John Passion is NOT OK. It's fine to present this piece, but it needs context. My experience had to do with idea that we all are complicit in the actions of the mob. No anti-semitism, yes to personal responsibility and examining your actions.