I'm a big fan of O'Reilly's multi-format approach. This is the correct end-run around proprietary stores.
Regarding this issue in particular, I don't see the problem with Amazon and others kicking their users out to Safari to do purchases, and thus as the purchase wouldn't happen "in app" it wouldn't be covered by this.
Not as smooth of a purchase experience, but not impossible to deal with.
The other alternative would be to tack on a 30% surcharge on any books bought directly through the app.