I agree there's more to the story as well, though I think for different reasons.
Everything I read, Vegas lines, everything had Newton as #1 starting the season.
I don't know how short the leash was. I don't know if he barely was #1. But it appeared he was.
Then he gets put in a certain protocol again. This protocol will remain nameless as I don't want to get banned or warned.
Once in the protocol again, rumors started, articles started and all of a sudden his 5 day absence opened the door and he might lose the starting job to Jones.
In my line of work there's no such thing as coincidences.
Newton caused them a headache, he had no intention of fixing the headache from happening again, he got the headache at the last minute.
The team IMO decided to remove the headache and see what the rookie has.
The only difference is, unlike Urban Meyer, they smartly didn't state they removed him because of not wanting to fix his headache problem.