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.
Them there quick fix miracles seekers are at it again. Those ridiculous people who want nothing more that some quick gratification, huh?
Maybe, they are people who are really desperate for a miracle, exercising their faith in God. Do you have a faith in God? Maybe they are just like you.