I don't believe this for a second. Sony is well known for spouting B.S. that is completely unfounded. They probably got rejected for using an IN-APP WEBVIEW control to open their store. If Apple was to make this change, randomly, most of the very top rated app store apps would be banned:
Kindle
Nook
(basically every eReader app, even Stanza for accessing Fictionwise)
Evernote
Netflix
Pandora
Skype
Hulu Plus
FarmVille
FT
NYTimes
Dropbox
box.net
(tons of other services accessible via App Store apps of their own and others)
As well as many other similarly purposed apps. There is no way Apple is banning eBooks as reading (of various forms, such as mail, sms, im, twitter, books, articles, documents, notes, etc.) is pretty much the #1 reason to use iPad and iPhone and we all know iBooks is a pathetic performer compared to Kindle.
The fact is that Sony is a competitor with Apple. Sony is full of talking heads that don't know what their priorities should be and will blindly jab at competition even while trying to ride their coattails. When, if ever, real details finally show up for what really happened I'm sure it will be a well established rule having been broken and Sony using it as a false alarm for crying wolf about Apple's app store.
I mean, really, how many times has this kind of nonsense come up (independent, unverifiable app store approval claims) and later we find out it was just lies? Way too often.