I agree with you.  When Manning started that rookie season, Indy knew that season was going to be a developmental season for Manning.  That they were not going to compete for the division or the playoffs.  
Broncos have to make the same type of decision now.  If they probably play Lynch, he is going to make his share of mistakes which will probably result in 3 or 4 lesser wins at the end of the season.  So the Broncos have to decide if they throw the towel on this season in the hopes of developing Lynch for future seasons.  Kind of like what the Colts did with Manning.
As far as Manning's accuracy, I don't remember what was written then.  But Manning was so driven, dedicated to improve.  So even if he had issues, he would have probably taken 500 snaps every day to overcome those mistakes.  I am not sure if Lynch is similarly committed.