Why do people care so much about Amazon? Amazon is a middleman, so why not cut them out? Magazines, Newspapers, and Blogs can go directly through Apple and keep their same 70% cut.
I highly doubt that Apple will ever pull a Kindle-viewer app, so your second concern is likely a non-issue.
That's the point, there aren't 2 middlemen. There is only one: Amazon. Apple wants to take Amazon's place by asserting their privilege over the platform.
Why doesn't Amazon allow iBooks to be purchased on the Kindle? They're in direct competition.
I use and love Amazon services, but I have a hard time feeling bad for them in this matter.
If content, quality and prices are equal between the AppStore subscription and the Kindle store versions, I have no incentive to buy from the AppStore when it's less feature rich than a Kindle version which can seamlessly sync and move between PC, Android and iOS. AppStore purchases are stuck on iOS devices, and the Kindle's display is the preferable reading screen for many people.
To be fair, it's not limited to Amazon either, B&N and the Nook are in the same situation.
Convenience, product visibility, uniformity of services, buying power, plus they assume certain risks on my behalf (dealing with shady/inexperienced suppliers, maintaining distribution channels, chasing refunds, notifying me of recalls etc). It's the same reason I go to a grocery store instead of making trips to a dozen or more local farms.
In the digital arena, product suggestions are becoming important too. Amazon has a fairly accurate profile of what I like, and can show me stuff I might like but would never discover on my own. Independent niche suppliers can't build that profile and they usually don't want me checking out their competitors.
There's also the consumer willingness to trade product rights for cost savings. O'Reilly sells non-DRMed PDFs of their books on their own site, or I can buy a DRMed copy from Amazon for half price. For a book that'll might be antiquated in 3 years, that savings starts looking pretty good.
"Current technology" is no magic bullet either. The cost barrier of the infrastructure is lower, but it still requires talent a supplier may not specialize in to run it. Selling your own product poorly is probably worse for you than paying someone else to do it well.