Amazon has already started discounting ebooks - some of the bestsellers are now cheaper on amazon in ebook form than on iBooks. That never happened before in Agency model, where price parity was a rule.
There is nothing inherently wrong with Agency model pricing; indeed it has been the norm since mp3s on iTunes 10 years ago. But Amazon competes on price, and Agency was a big wrench in those plans. Now that they can do anything they want with digital pricing, they're applying the stake in all other ebook retailers hearts. Will be fun to watch.
I speculate publishers will hate this. eBooks were one of the last digital media where value hasn't become completely pulvarized (see: Apps, MP3s). Though, its certainly possible physical book sales could be bolstered by this.