I contacted the Missouri Wine Advisory Board. They weren't helpful. I got ahold of someone at the main office for the state Alcohol Control division, and he was really helpful. That guy said that it's the position of his agency that statutes take precedent over regulations, and that if state law says I can use honey in my winery, then it doesn't matter if the regulations don't specifically state that I can.
He also told me that my county health inspector is the one who will actually be inspecting the facility, and as long as they're happy with the facility, the state is happy. It seems like the state doesn't particularly care about regulating. Yay, Missouri!