Embedding the ibook in the app would not be possible, but cross-linking would. That's not to say cross-linking would be easy, or do everything you mention. Each ibook in a user's library has an ibooks: url that will open that book. The problem is knowing that URL, because I believe it's not unique across devices (could be wrong about that, but probably not). And I think you can launch apps from links anywhere, but I don't know the specifics of how you could do deep-linking.
In any case, you might look at ibooks author which supports the use of Apple's dashboard widgets. You can use dashcode to create embeddable HTML 5 apps in an ibook file.