I think this is a trainwreck in the making. What really annoys me is that you can link to legitimate paid books but then if your website users go on "free ebook benders" within the 24-hour period your affiliate cookie is active, you could end up losing all of your commissions for the month.
It's going to kill the free ebook referral sites that depend on commissions...lots of bloggers and reviewers could get caught up in this mess.
Ultimately, I think this is one of the dumber moves I've seen Amazon make.
The free ebook sites and links have been a HUGE part in helping Amazon become so dominant in the ebook industry.
If those sites decide "We're not going to sit back and take this," they could switch their affiliate programs to Smashwords (11%+ commissions) or Kobo (5% commissions) and help push those sites to much higher traffic and sales levels.
At least that's what I hope happens.