I have little sympathy for the 0.1% of affiliates who will be affected by this.
If you want to give away free ebooks, by all means go for it.
If you want to give away 25,000 free ebooks a month on someone else's bandwidth and expect to get paid for it, that's another story.
I'd also guess that if the current affiliate program was working as a loss leader, Amazon wouldn't consider rolling it back. Keep in mind that no matter what you think of Amazon, they are experts at data analysis. They're more than capable of targeting a handful of unproductive sites.