Two scripts were turned in for the project - a first one by George Nolfi and a second by Josh Zemuter. The site says that no one likes Nolfi's version, but that Greengrass was not consulted by the studio in the hiring of Zemuter.
It will be interesting to see how this will affect Matt Damon's involvement. He's close to Greengrass and also starring in the director's upcoming Green Zone. Nolfi also wrote, and is directing, the Damon-starrer The Adjustment Bureau.
The Playlist does add that walking away might be a "typical Paul move" and that he possibly could be back on the project in a few months.
UPDATE: Paul Greengrass has released the following statement, confirming his exit and addressing the above:
"You won't find a more devoted supporter of the Bourne franchise than me. I will always be grateful to have been the caretaker to Jason Bourne over the course of The Bourne Supremacy and The Bourne Ultimatum. I'm very proud of those films and feel they express everything I most passionately believe about the possibility of making quality movies in the mainstream. My decision to not return a third time as director is simply about feeling the call for a different challenge. There's been no disagreement with Universal Pictures. The opportunity to work with the Bourne family again is a difficult thing to pass up, but we have discussed this together and they have been incredibly understanding and supportive. I've been lucky enough to have made four films for Universal, and our relationship continues. Jason Bourne existed before me and will continue, and I hope to remain involved in some capacity as the series moves on."