I agree with everything that you wrote, except the very end. Nearly all the coaches in the league, imo, would have waited until the off-season and the OTAs to increase the emphasis on the Pistol as Harbaugh has done and install Kaepernick as the starting QB. I really cannot think of another coach in the league that would have switched QBs in midstream as Harbaugh had done, given that the playoffs were on the line at the time as well as the expectations in the 49ers organization that this was a Super Bowl team. The expectations were extremely high for the team at the time of the change. It was a huge risk that Harbaugh took, imo, and it worked.
I see a lot of pooh-poohing of Alex Smith as a QB on this board. Frankly, this pooh-poohing is borne from ignorance of not watching the 49ers on a regular basis. Smith's 104.7 QB rating was no fluke. The guy is a very good, maybe not great, but very good NFL QB at this point in his career. If he goes to, say, the Arizona Cardinals next season, he will make them a much better team. I wouldn't be surprised to see three NFC West teams make the playoffs next season if Alex joins the Cardinals, which is what I suspect will occur.