Even better, Smith actually lead the league in QB rating and completion percentage. He was having his best year as a starter, and he gets benched.
It goes back to what Drew Brees said Flutie told him when he first got to San Diego, "Never let another quarterback get on the field"
And thats what happened. Harbaugh saw what Kap could do in that Bears game, he litterally added to the playbook. As good a season Smith was having, he still limited what that offense can do.
My biggest question was, what will Kap do when they take away his running ability. That question was answered with the Falcons game. Most people point to his win over GB as his most impressive performance, but as a QB, in my opinion it was the win over the Falcons. The Falcons succeed at taking away his running ability. But after some adjustment, the disciplined reads he made was outstanding. He beat them with his arm and their running game, utilizing the pistol read option to it's full capabilites. I honestly dont know how you defense that thing. Atlanta did everything you are supposed to do, they kept him in the pocket and played zone coverage, but then Vernon Davis, Moss, and Davis ate those zones for lunch and Gore cruised through those gaping holes.
Ask any defensive coordinator who they would rather face on Sunday, Smith or Kap and guarantee you all of them will say Kap.
It was a bold move from a public relations perspective, but from a football perspective, it was a no-brainer.