Short answer: Publishers were too weak individually to challenge Amazon's ebook business model (the wholesale version). If all the publishers colluded to stop selling to Amazon, that would be a violation of the anti-trust act. Apple comes along and writes contracts with each publisher such that in aggregate the contracts provide the cover to do exactly what the publishers could not do on their own.
The harm in the short term was to Amazon - under threat of being cut off by every publisher, it would have forced Amazon to move to a different model of pricing. The follow on effect would be to raise prices for all consumers.
The harm in the short term was to Amazon - under threat of being cut off by every publisher, it would have forced Amazon to move to a different model of pricing. The follow on effect would be to raise prices for all consumers.