Even though Smith is getting a fairly raw deal right now, Harbaugh actually did him a huge favor by giving him another chance. Smith is going to be able to go out onto the market with the world seeing that, while he won't exactly set the world on fire, he can play quality, efficient football. There will be a team out there that needs a starter or someone to compete for the starting job, and the last season and a half have likely helped turn Smith into a viable candidate for that instead of being forever doomed to the role of second-rate backup.
Edit- And Timby
pretty well beat me to the punch on that.