Apple's service agreement actually demands price matching, which means a content provider must provide their best price available through the app. It is probably possible to charge more for an "iOS edition", but Amazon specifically has a standard publisher contract that requires them to charge the same price on all platforms.
Which is a sensible clause for Apple, so that Amazon can't go and say "all books bought on the Kindle device are 50% off what you pay when you buy the book on the Kindle for iPad app" to drive device sales.
You have it a bit backwards, the kindle is there to drive ebook sales, not the reverse. Apple only added the clause when they added the mandatory in app sales with the 30% tax - if amazon had any intention of doing something like that you'd presumably already have seen that behavior on the iphone or pc or osx or android.
Whats in it for the companies? Run afoul of Apple and get locked out(rejected or worse, approval gets delayed for months) of the tens of millions of potential customers? This has already happened for many apps.
No one except very small companies are going to go this route, if any.
Make a beautiful logo out of it, constantly reminding people that the price increase is due to Apple.
... and at the same time offer a clue that they can get the same services/goods cheaper on another platform (say... Android).
Would that help to drive users to understand how bad Apple is and hopefully start a public uproar?
Perception right?