Nah, he's always been pro Allen. It was the one thing that gave me hope when we drafted him (I was one of those wary of signing a "toolsy" QB over an NFL ready one). Pete said he had the potential to be one of the best, it would be about his growth and the coaching, and he lauded McBeane for getting him.
Prisco was always dismissive to the point of being offensive about the Bills right up to drafting Allen and having seen a season of McD in the job. Since then he's been pretty accurate about the overall progress.