Yeah, we were thinking about that issue - as to what would be best. Actually, some people (including my partner, who is an observant Christian) do sing Bach partly for the words and are moved by the New Testament text. I know my partner would not feel comfortable substituting the biblical text for meaningless syllables, and omitting the whole chorus seemed more respectful of the words and music than changing them. In fact, he said that the bits before and after the notorious chorus were both in D major, so it wasn't a musically weird decision. There are recitatifs before and after, so the Evangelist part is just sung continuously.

Having said that, one of the suggestions people made was to just change the cast names from "Jews" to "Angry Mob". By doing that, you're not changing the lyrics at all - just the character definition in the libretto. This seems like an ok option for performers who wouldn't want to omit it altogether.