The chickens that weren’t kosher or schechted properly are sold to non-Jews. So it isn’t wasted and the tzedaka profits from that as well. Additionally, even on a farm there is a certain percentage of spoilage. The spoilage by kapporos isn’t a lot despite the anti-semites’ (both the Jewish and PETA variety) lies.
Sam: The vast majority of kapporos centers treat the chickens halachicly and appropriately for animals and are appropriately taken care of.