I can sort of understand where Apple is coming from in this. They provide an ecosystem and apps live within their ecosystem.
That being said, I can't see Amazon or any other big player rolling over on a margin of 30%. This is the problem with one fixed margin: it works well for apps and music but not necessarily for other things.
You see the same problem with the Mac App Store: smaller devs love it. Will you see Microsoft Office or Adobe Photoshop on it? I doubt it. 30% is just too much for those big players to hand over.
I consider Kindle to be a key part of my iPad experience and I can say if the end result of this is that I can't read my Kindle books on my iPad I will be pissed. I bought them specifically because I could.
Ultimately though I think Apple needs to give up control here. They should provide a payment infrastructure and if it's comeplling, people will use it. If it's not, they won't. But don't make me a casualty of war in the names of the the consistency of your 30% cut.