A couple things as far as I can see...
1) Wouldn't it be pretty easy to just remove the 'store' link from the apps (like Kindle app)? Most people who have been buying Kindle books probably do it directly at the web site anyway. All that button would be doing, would be linking to the web site, as you don't buy the books through the app anyway.
2) Same for Netflix... the people could create their account before using the app, and then the app would just have a 'log-in'.
So, neither app would really have any issues, even if Apple did really push this. However I'm hoping Apple is smart enough not to push it. I think if Netflix and/or Amazon pulled the apps, the popularity of the iOS devices would take a pretty big ding.
Since there is really nothing else, I suppose I'd have to stay for now, but I'd be horribly miffed at Apple for forcing me to carry both a iPad and a Kindle! I might seriously consider the competing tablets when they come along if that were the case, as carrying multiple devices kind of defeats the purpose.