Yep, you have to look at the entire body of work. Up until the bye-week, the statement that he was the worst freshman starting QB ever at BYU was entirely correct. In fact, he was the QB ever at BYU, up to that point.
But the season didn't end at the bye-week. Jake got much better. He played much better. By the end, he was a very serviceable QB as a whole and just looking at the last five games, he was playing at a level commiserate with where a starting BYU QB should be.
By the end, he did a lot of things many QBs at BYU never did. He now has as many bowl wins as Detmer, Sarkisian, Bosco, Young, and Beck. Was it a great year? Not when taking the whole of it. Was it a good year? Probably not when taking the whole of it. Was a necessary year? Probably.
Does it bode well for the future? I'd like to think so. Remember, don't get caught up in revisionist history. Just because he turned the corner and went from gawd-awful QB to very productive QB, doesn't make the criticism of his play when he stunk any less valid than the praise he rightfully deserved when he played well.
So he was both the best and worst freshman QB at BYU. The two are not exclusionary nor contradictory.