The kid played in one game...and caught the apposing team off guard. What has he done besides that one game? Smith isn't spectacular...but, his QB rating was top 5. I don't think you bench your vet after an injury...and force guys to take sides in the locker room. Harbaugh should know better.
Now, Smith knows that you're not in his corner. If Kaepernack falls on his ass...Harbaugh is screwed.