As someone else said before, WOTC will need to address this issue and 'spin' it so it does not damage 5E's chances.
When you lose one of of your main designers (on a team of three), it is not a negligible loss. This is major and the timing of the departure means that the conflict, whatever it was, was major enough to cause a professional to drop a project mid-run.
Since I believe that 5E being started up so quickly stems from 4E lacklustre results, both in terms of $$ and in terms of enthusiasm from the gamer community, the fact that WOTC did not bend on the issue with Cook leads me to believe that whatever the issue is, it must be MAJOR.
Surely WOTC realises that 5E is their last chance to 'redeem' DND and if they fumble now, DND will continue to loose steam and probably never recover.
About the only issue I can see that corporate suits are this stubborn about would be the OGL. The suits see Pathfinder and are determined never to create their own worst enemy again, failing to see that their stupidity is what is feeding their enemy to begin with.
Pure speculation, of course, but what is the Internet for? Well, speculation and the biggest porn distribution system in the history of mankind.