The Dougs certainly are backing EJ 100% probably because they don't believe it's time to rattle his confidence yet. They took him knowing he was raw and was going to take some time to develop. I don't think they even wanted to start him last season until it became obvious that Kolb's head is one hit away from being mush.
Sure the Bills gave up next years 1st but they got a HUGE talent in Sammy Watkins. A guy who is physically talented but also has the work ethic to become the best. He is about as sure-fire of a star as you can find in the draft. Also, there are a number of ways to bring in a possible QB1's besides your slotted first round pick in the draft. You can trade back into the first round and grab a guy that has slipped, like the Browns with Johnny Football or the Vikings with Bridgewater. Or you can trade away future picks for a QB that comes up on the trading block, or you can sign a veteran in free agency.
The Bills roster has made huge strides under Whaley and Marrone. I'm willing to see how things go before bringing out the pitchforks. If you don't get a franchise guy like Peyton or Luck to fall in your lap then you have to develop one. Guys like Big Ben, Eli, Flacco all took time and they were playing with much more talented rosters than the Bills put out there last season. If you identify a guy you think can be a franchise guy then you stick with him and stay the course.
That's what the Bills have decided to do. Will they be right? I don't know, but it's going to take time to get the final answer. Maybe not even until next season.