one way Apple could respond to the e-book judgement

Assuming they don't win a reversal of the e-book judgement on appeal, Apple still has options.

One option would be for them to move the preponderance of the code in the iBooks app into iOS and OSX, making it available through a new high-level API, so publishers could easily build their own apps based on the Apple code, providing a relatively uniform experience for users, and an opportunity for Apple to incorporate indexes to the collections in these other apps into its own iBooks app, or into a new utility that treated iBooks as just another instance of the category.

Presumably Amazon would also take advantage of this code to build their own iOS/OSX reader.

As for sales, besides the iBooks Store, Apple could offer to host, for a nominal fee, publisher-specific stores that worked with the apps based on Apple's iBooks code and used Apple's payment system, as well as allowing those apps to work with non-hosted stores.

The advantage to Apple is that it would make it possible for them to make their platforms clearly superior for e-book reading, through API improvements that would improve the behavior of all apps based on that API, including Amazon's, giving publishers an even better reason than they already have to be on Apple's platforms.

Smaller publishers and independent authors would still choose the iBooks Store. Medium-sized publishers might opt for their own stores, hosted by Apple. The largest publishers would most likely prefer to host their own stores in-house, but still take advantage of Apple's e-reader code.

While it's unlikely those opting for publisher-specific stores would agree to Apple's usual 30% cut, Apple could set a lower commission for hosted stores, say 20%, and a still-lower commission for independent stores, say 10%, and continue to garner revenue from the e-book business.

How Apple could monitor sales via independent stores and collect their 10% isn't clear to me, but I'm fairly confident they could find a way of doing so, and by making this their standard approach to the business they could at least put Amazon in the position of having to choose between coughing up 10% of sales or doing without access to the API that enabled a uniform reading experience.