It's all very well to burn her at the stake, or make her dance in red-hot shoes until she dies, but that's really the same question, slightly rephrased. They couldn't do it if they weren't in human shape -- and their subjects could be handled the same way.
So, in best fairy tale style -- the evil sorceress can really only harm you when you are in a vulnerable state: left home. are preparing for the wedding, etc. A liminal state, in fact.
Then, of course, I have to figure out why two characters who are going to remain in hiding for fear of the evil sorceress do so, when they have long been married. I suspect that it shall have to be out of fear for their children, who are in the danger zone. Unless I decide that they will have a third child.