There has been much debate over the Kaparos custom for many years.
Some of it has been about the very basis, the theory of the matter (e.g. is there a question of foreign Darkei Emori practice, as the mechaber of Shulchan Aruch maintains), while other parts of it was about the actual activity, how things worked out on the ground (e.g. was the shochet tired, calling the shechita into question, tzaar baalei chaim concerns). Now, it seems that there is a new issue raising additional concern about the practice.
Evidently, in some places, the chickens, after shechita, are just treated as refuse.
While in the past it was assumed that the chickens were ultimately used as food, which seems to have usually been the case, when people were not so affluent, and were used to kashering (salting, removing blood, etc.) chickens at home themselves, nowadays, on the other hand, most people are used to the modern convenience of buying pre-kashered chickens and are not versed in, or comfortable with dealing with kosher fowl preparation themselves. The chickens nowadays are relatively inexpensive as well, due to mass production, and modern scientific advances, with G-d's bounty.
An additional difficulty is that most kaporos centers are not near the giant poultry plants where kosher fowl is usually prepared. So even if people would want to give their chickens to the plants for the balance of the necessary preparation, distance and other difficulties present significant barriers to such action.
So now that it has been revealed that fowl (the extent is not known, but a significant amount of chickens have evidently been involved in the past) are trashed after the ritual, which invokes the issue of Bal Tashchis, the prohibition against wasting things, particularly food, should those people who do it with chickens reconsider their participation?
This question was the subject of heated debate recently at a Chabad-Lubavitch website.
One writer called for using money instead of chickens, as some others have done for years. Another writer claimed, in response, that trashing the chickens does not invalidate successful kaporos.
Many commenters weighed in with various thoughts and suggestions.
Let us hope that people take such considerations into mind, and avoid a situation of יצא שכרו בהפסדו (gain outweighed by loss) in this season of repentance.
P.S. After Yom Kippur we learned of a new Kapporos scam - Halal Kapparos.