I think it's about time that someone has publicly come out with this.
Yes, this type of abuse (and worse) does occur in factories all the time, but at least in factories they are not claiming to do this as a way to absolve themselves from sin. Also, in factories what goes on is behind closed doors, so there is no apparent Chillul Hashem being made. (Despite the fact that McDonald's factories commit far worse abuse.)
Every year by Kapparos I am handed a 3/4 dead chicken by some 12 year old kid who pulls it aggressively out of a crate by its wings. One year I had my chicken die on me by the time I brought it to the Shochet. Of course, I had to do it all over again. (At least they had the decency to give me a new one. They threw the dead one under the truck like a soccer ball.).
The only way to do this "humanely" would be to get taller crates so that the chickens don't have to have their heads squashed, put less chickens in a crate, feed the chickens and give them water every few hours, and keep them in a shaded area.
Of course, doing that would raise the prices by $5 per chicken...