I got a call from Consumer Affairs today after emailing them last week at longing4piedmont's suggestion. The explanation was pretty much the same I had gotten when I called them. The Air Marshall specifically wanted my seat, nobody had been upgraded at the gate and my A fare was amazingly inexpensive.
They offered me a confirmed NA upgrade for the inconvenience and I'm very satisfied with that. I do think they could have handled the situation better though. If the gate agent had been able to issue an upgrade certificate or if Consumer Affairs had offered it the first time I called, my complaining would have been kept to a minimum.
All in all I'm happy with the outcome. Like I said in my first post I've come into contact with some terrific US employees. Some of the flight attendants are amazingly funny/thoughtful/interesting and I look forward to flying with them again.