Echostar/DirectTV DVRs are rented, rather than purchased. So the court there was ordering Echostar to disable features on a device it still owns.
That's a whole lot different than ordering that devices which were sold in good faith to people who were not party to the lawsuit be forcibly recalled or disabled -- with no mechanism for the owners of the devices to protest or make their interests heard.
Now, no doubt the legal issue here is that you don't really *own* a kindle file like you own a book. I bet in the TOS somewhere Amazon says that they are really selling you an indefinite but conditional and revokable lease on your copy of the book. I'm sure they trumpet the lack of real ownership to the publishers as a major benefit of the format.
If the terms said that when you purchase an 'ebook' on the kindle, you actually do in fact own that file. I can not believe that they could have gotten away with deleting the books; I can't believe the courts would endorse let alone order such an action.