The way the 49ers lost their whole defense didn't have much to do with stupidity that leads to the egg on face you mentioned... but since you brought it up...It didn't get missed. The evidence with which you supported it got dismissed. The question is whether you are gonna just stick to it after the evidence got dismissed.
Fact: Alex Smith was doing a good job as the 49ers QB, got hurt, and the coach defied the general rule that you don't change starters as a result of an injury by giving his job permanently to the backup. The 49ers now look stupid since the coach AND the replacement QB have both subsequently been run out of the league and Alex Smith is leading a very strong contender.
I suspect that your position on Alex Smith has more to do with the faceful of egg the 49ers are wearing than his actual performance.
Alex Smith was doing a mediocre job as the 49ers QB. If you want to call it a good job, fine I guess that's defensible, tomayto/tomahto. You've pointed out before that 49ers fans tend to have lofty (possibly delusional expectations) and I would say that's also a fair critique, especially when it comes to QBs. So I can't deny that Alex Smith was a perfectly fine QB for the system the 49ers were running, ie Ground and Pound. But he didn't have any explosive playmaking ability... or at least he didn't demonstrate it on a regular basis. Harbaugh saw lightning in a bottle with Kaepernick, but then his relationship with the owner went south.
As for the 49ers being stupid... again, you've got me there. Losing Harbaugh was stupid. I can see why Harbaugh went with Kaepernick though... He was an exciting change of pace for humdrum Alex and his 200ish yds with 1 TD week in week out. But yeah I'm sticking with 251yds and 1 TD is mediocre. If you disagree with that then we disagree... its rare but I'll live.