IMO this is as much about Sammy Watkins as it is about EJ.
Everyone saw Sammy "take a play off" two weeks ago after Goodwin got blown up, and then come in and drop two more passes yesterday, plus wisely decide not to lay out for a floater in the fourth quarter. EJ has been putting receiver after receiver into harm's way and the Bills probably decided they want Watkins on the field for the rest of the season... something that is unlikely to happen with EJ under center.
Whether EJ is done is something I'm not really concerned about. I'm just glad we finally treated him like a player who needs to earn his job, rather than as a first-rounder who needs to play his way out of one.