I honestly don't understand how you can feel this way about the case.
I have a couple of points I want to touch one.
First, yes there have been many critical analysis and essays written about the Harry Potter world that were published. The key thing here is that they were critical analysis and original essays written by the people who then published their books. This is wholly allowable and often an encouraged out come because it generates interest.
Now, while the Lexicon does have critical analysis and essays, these were not written by Steven Vander Ark, they were written by a host of volunteers (a few of whom I know). These people were told that their contributions were not going to be used, that in fact (per RDR) none of the original essays and analysis on the site were going to be used. A direct conflict of what RDR originally told the WB lawyers when they said they could print the Lexicon website if they wanted a copy of the book.
Also, the Lexicon wasn't completely compiled by Steven Vander Ark, it was a labor of love that a LOT of volunteers took time to compile, and I know that many of those people have asked that their work be removed from the Lexicon site in light of the litigation (I know for a fact that this is true for Mrs. Muggle on livejournal, and one other that I can't remember off the top of my head).
So, no essays from the site, and a ton of complied quotes from the book. That leaves what? The whole sale cut, copy and paste job from the books into a alphabetized order. Mmmm sorry, but that all was written by JK Rowling, not Steven Vander Ark.
JK did not have a problem when the Lexicon was a free website, and honestly, consider the amount of copyright information on it, we (as fans) were incredibly lucky she allowed it to exist. She has ever been an advocate of the fans and what they create.
This whole situation is just a travesty, and Steven Vander Ark should've known better.