They became "exotic pets" when they stopped being farmyard livestock. In the pet and vet trades, anything that isn't a dog or cat is considered an "exotic." This includes chickens, rabbits, mice, rats, hamsters, and reptiles.
As for whether dogs should or shouldn't be allowed in public places such as pet stores, I am always saddened when they are banned from a place where they were previously allowed. To me, it states that the responsibility of pet owners is failing. I rarely take my dog with me to stores, but it can be a great training opportunity for him as well as a mentally stimulating change of pace. I don't allow him to run nilly-willy at the end of the leash. He is kept on a relatively short leash and expected to pay attention to me. For us, the main point of going to a store is to get him used to focusing on me in public situations with other people and dogs around. I am constantly scanning the area for potential problems and I react accordingly. If I see an idiot with a 100lb golden retriever pulling him down the other end of an aisle, we will avoid that aisle so that we don't have to deal with an out of control dog. If people are so rude as to allow their dogs to approach mine without talking to me first, I will body check the other dog by stepping between them and my dog and move my dog so that they don't meet. These are skills that any dog handler who chooses to take their dogs in public should know well and utilize. I personally do not allow my dog to approach a stranger unless they show very specific interest in meeting him, even if my dog is interested in mooching treats off of them. Yes, there is a risk of my dog picking up some sort of disease at a pet/feed store. But it's not really that much more significant than his risk of picking up a disease at the local park or on a walk around the neighborhood where dozens of other dogs are walked every day. That's why my dog is vaccinated, to minimize the risk. I have never once had a problem at the local feed store we go to and although the risk of a problem is much higher at the
Petsmart due to the fact that a large percentage of the people who do take their pets there fall into the "idiot owner" category I haven't really had any problems there either (of course, I try to avoid going during peak shopping hours such as weekends in order to minimize the risk of running into said idiot owners).
I personally wouldn't take a chicken to a store, but in this case it was a better choice than leaving them in the car and I personally fail to see how a couple of chickens confined to a carrier in the basket of a cart pose a health risk or physical danger to anyone. I also think the health risk to the birds was minimal, certainly no greater than at the auction they had just come from.