Birds bred specifically for research are exempt from the USDA Animal Welfare Act; however, all other birds used ARE regulated by the AWA. The only exemptions to the AWA are mice of the genus Mus, rats of the genus Rattus, livestock used for agricultural research, and birds bred exclusively for research, all other birds are regulated. In addition to the list are non-warmblooded animals and invertebrates.
That came pretty much directly out of my notes from my laboratory animal class that I had to take to get my veterinary technician degree. That class covered, heavily, on state bodies, regulatory agencies, and their requirements/regulations.
I do agree with you, though, I do not see reptiles being added to the AWA list anytime soon based solely on the fact that most people do not care about them. They are largely considered emotionless and generate more fear than any other animal on the planet, which is unfortunate.
I hate reading these articles and these obscure cases that force me to question the agencies I am supposed to support, being that I am in an animal care field. I was taught in school to trust these agencies and that they are for the greater good. I know that animal conditions would be worse off without APHIS and the USDA but what they are doing to those people is wrong. But It sounded like to me that the rabbit farm would have been fine if they were USDA certified. Shrug. Doesn't make it right.
As far as, "killing our industry," it would require us to become USDA certified, possibly, but it wouldn't kill those who are breeders. It'll mandate cage space, ventilation, heat, humidity, and probably a list of other things but you should be practicing those anyhow. If it does happen, it will make things more difficult and require us to jump through hoops but it's really not THAT bad. All of the animals I worked with at school were regulated. I had to deal with the inspectors being there. They can be bastards but their requirements are not unrealistic.