Well it looks like that spec script was more of a way to replace Whedon than to simply protect their interests as WB originally said.
Here's the scoop, direct from Joss himself:
You (hopefully) heard it here first: I'm no longer slated to make Wonder Woman. What? But how? My chest... so tight! Okay, stay calm and I'll explain as best I can. It's pretty complicated, so bear with me. I had a take on the film that, well, nobody liked. Hey, not that complicated.
Let me stress first that everybody at the studio and Silver Pictures were cool and professional. We just saw different movies, and at the price range this kind of movie hangs in, that's never gonna work. Non-sympatico. It happens all the time. I don't think any of us expected it to this time, but it did. Everybody knows how long I was taking, what a struggle that script was, and though I felt good about what I was coming up with, it was never gonna be a simple slam-dunk. I like to think it rolled around the rim a little bit, but others may have differing views.
The worst thing that can happen in this scenario is that the studio just keeps hammering out changes and the writer falls into a horrible limbo of development. These guys had the clarity and grace to skip that part. So I'm a free man.
So the two writers of the spec script - newcomers Matthew Jennison and Brent Strickland are now in a position to take the controls of the invisible jet and either make this film a soaring success or watch it crash and burn.
Its going to be interesting, considering that according to the THR article, the Jennison-Strickland script is set against the backdrop of World War II, while Whedon's script was set in the present day. How this is going to work is anyone guess.