What are you replacing them with?

I was already splitting my ebook purchasing between the Apple bookstore and Amazon.

From this point, ebook purchases will be through Apple or a purchase of the real book. I kinda miss the feel of a real book too so that's a nice change. If I need a digital copy, and it's Amazon exclusive, then I'll be using "other sources".

Out of curiosity (I haven't purchased ebooks from either source), what makes Apple more reliable than Amazon?

They have yet to pull a stunt like this. As far as I'm aware, they are unable to remotely modify Apple devices. Until proven otherwise, I trust them.

Just wait.

https://iphone-services.apple.com/clbl/unauthorizedApps

Edit: And don't forget the remote wipe feature in Find My iPhone. http://www.wired.com/gadgetlab/2012/08/apple-amazon-mat-hona...

I'm a little dubious too, but Amazon has a track record of doing things like this (The Animal Farm/1984 fiasco), whereas Apple seems to respect that they've sold their customer something.

Keep them, and manage Kindle content of DRM-free books via Calibre.