Dan Frommer has a good take on how these changes are bad for Apple's customers as it leaves them with an inadequate user experience. I agree with Frommer for the most part, due to what I have seen in my own household.
My wife bought an iPhone 4 as soon as it was available on the Verizon network. She has taken to the iPhone like an addict to a banned substance, rarely putting the thing down at home. She has explored the App Store on her own and installed many apps that she uses a lot.
One of the apps she installed was the Kindle app, and since then she has been reading ebooks on her iPhone almost exclusively. Forget that I tried to convince her years ago that ebooks were better than the paper variety, especially on a phone that is always with you, it took doing it herself to convert her reading habits.
Today she is not a happy camper, meaning she is an unhappy customer of Apple's due to the changes Amazon was required to make to the Kindle app. She can no longer easily access the Kindle bookstore on her iPhone, she has to manually open the Safari browser and shop like she would on the desktop. She doesn't like doing this given how easy it used to be, and each time she does she gripes loudly; but she does it. She has no intention of switching to Apple's iBooks just to make buying ebooks easier as she's already built up a library of Kindle books. She is the type of customer Apple loves, a loyal one, and now she's ticked off at Apple over the change.
I understand that Apple has the right to handle its own App Store anyway it sees fit. I agree that it had every right to change the way in-app purchases are handled, thus forcing the changes to competing ebook reader apps. But in the long run I am not sure it is in Apple's best interest to have done so. The good (loyal) customers are not going to switch just to make it easier, so Apple is not gaining anything. It is just making its own customers unhappy at Apple.