Well, first, Cartman's always making jokes about Jews. Once he says about Kyle's cousin after Mr. Garrison tells him to concentrate: "Maybe they should send him to a concentration camp!" There was an episode in which Cartman dressed as Hitler for Halloween, and another in which he actually tried to exterminate the Jewish race by using unassuming fans of the Passion of the Christ (I assure he got grounded afterwards.) There was also an episode, "Deathcamp of Tolerance," in which the boys were sent to a death camp to learn tolerance. It was a huge parody of Holocaust portrayals in movies: the kommandante had a thick German accent and they had to do forced labor (like fingerpaint pictures of multiethnic people holding hands) In a recent episode, they even made up a thing about a bag of Jew gold, which Jews wear around their necks. Cartman kept demanding Kyle to hand his over, and finally Kyle did. Thanks for the description. Again, I haven't seen the show so let me ask you further;
Was the parody making fun of ones faith in Judaism or was the parody making fun of the intolerant who would mock that faith?
Was the parody making fun of the Jews in the concentration camps, the pain that they endured and the deaths many suffered (including entire families) or was the parody making fun of the freakish Nazis who caused all of that?
It was doing the same thing as the Mary thing: it was seemingly poking fun at the religion, but deep down it was making fun of the latter things you mentioned. Same with the Mary thing: on the outside it seemed to be making fun of Mary, but really it was just making fun of people who flock to miracles just for a quick fix.
With South Park, you can't just look on the outside level. You have to dig deeper and find the true meaning behind the humor.