Big publishers did not object to Amazon selling for below list because it would impact Apple. They objected because they thought selling books at a discount would cause consumers to expect a lower price and they would no longer be able to sell higher-priced books. This is just what's happening right now. Amazon prices books very effectively and even more signficantly, Amazon has opened the marketplace for book sales to self=published authors and to independent publishers who are trying new models. For example I'm CEO of Booktrope which has a new model that produces ebooks that can be sold in the range of $2.99 to $9.99. (We pay a higher percentage royalty of authors in view of the lower prices.)
Amazon primarily but also Apple and Nook have opened up huge markets to us and our books are available broadly to readers. It means that big publishers will face competition from us, publishers like us, and self-published authors, and it's not going away.
The only way for the big publishers to avoid that would be to somehow block out competition including self-published authors and smaller, more efficient publishers who can produce ebooks at a lower price point. It's not going to happen so big publishers are at a crossroads and we should expect them to adjust or they will face continuing decline in sales.