I'm thinking that this could be the case. What was the disease/cause of the Patient of the Week's syndromes? Maybe they tried to tie in something he was doing in the CM practice (like maybe an allergy to some type of oil or incense) but realized that it wouldn't make much sense so they re-edited it and as Shad said, the altar somehow survived in the final cut.
I thought of the editing possibility, too. And I thought they were going to go with an allergy to an incense or something like that. But no.
[SPOILER ALERT!] The patient's problems ended up being caused by a combination of his secret steroid use and some hemlock that the "king" of the ren faire had made all the knights eat (mixed in with all sorts of other stuff like cow eyes). Nothing at all to do with his practice as a witch.