I'm sure you know that (for example) the Kindle iOS app uses an ebookstore that's in a browser, not the app. The app only contains a link to the ebookstore, not the store itself.
As I understand it, if you remove the links leading from the app to the website then the app will be perfectly fine under Apple's current rules.
Edit: My source pointed out that I neglected to mention a important detail. You can still sync the app with the ebookstore which means you could buy a Kindle ebook on the website and download to your iPad from inside the app. I had assumed everyone would figure that out, but perhaps it's better to state it.
This is newsworthy because Apple created this loophole only in the last couple months. It marks Apple's third shift in policy since this started 6 months ago, and this is the rule that will let the ebook apps stay in iTunes.
But don't take my word for it; go download the bol.com reading app. It was approved on 15 March and it's missing the link to the Bol.com ebookstore. I'm told they had to remove it in order to get Apple's approval.
I'm a little surprised that hardly anyone noticed (aside from my source and a Dutch ereader blog). And I really mean it when I say that this was largely unknown; I ran this by a couple app developers and it was new to them.