Looks like Willem Dafoe will be in Beyond: Two Souls after all. Proof is in the pudding below.
So, while not a denial, per se, it was generally assumed at the time the answer was “no”.
Dafoe will take on the role of Nathan Dawkins, a government scientist working with Jodie, played by Ellen Page, to analyze her strange powers.
Below is a gameplay trailer showing an early scene from the game in which the two characters meet for the first time. There is also a video with Dafoe discussing his role in the game.
Beyond: Two Souls will release on PS3 October 8, and the US PS Blog has information on GameStop pre-order incentives for the US and Canada through here. You get upgraded to the Special Edition at no cost when you pre-order.