Aunt Bea, I've frozen mine after they were baked first.
Chief, not trying to offend here, but if your DW is going to act a bit like a kid at the table not wanting to eat your good cooking, you'll have to feed her like one. When you make your filling for stuffed whatever for you, stuff a small casserole dish for her with the filling - before you add your onion. That way she can have basically the same supper you are, only without the unappealing "shell". Fix whatever easy veggie makes her happy, like canned corn or frozen peas.
"Cooking is the art of adjustment". ~~~Jacques Pépin