I think the point was that everybody was saying Kap gives the niners the best chance to win when he actually lost the game for the niners. I know you may not see it that way but a safety is nobody's fault but the QB's. Also a fumble that gets returned for a TD is not a good thing. He had a chance to win a game where Smith could not and he couldn't do it either . Kap is the future but he sure as heck isn't the present. This isn't the Eagles we're talking about who you just throw some players in because the season is lost. The Niners had a legitimate chance at going to the superbowl and now in my opinion, are screwed.
But he didn't lose the game for them. It was a team effort (missed FG, defense not making stops and conservative play calling). Anyone making this argument is assuming Alex Sux would have won that game and that just can't be assumed.
Concerning the safety, it shouldn't have been one. According to Mike Perriera (who I assume should know the rules), the playing field extends to out of bounds when viewing weather the ball got past the line of scrimmage. It's not where the ball went out of bounds. Based on that, the ball got past the line (clear on the replay) and should have not been a safety. So Kaepernick actually made the right play, but due to the lack of knowledge by the on field refs (not sure why they didn't or couldn't challenge), it was called one.
Concerning the "fumble", it was actually a bad pitch, but one that could have been handled by Ginn. While the execution of this play was poor, I question why it was called in the first place at that point in the game and that part of the field. Very risky. My guess is that Kaepernick didn't audible to that play, so it was more than likely called by the OC. That's just pure brain lock or trying to show how smart he is. Either way, if you're not gonna pass in that situation, run a conservative play and call it good. Have to put that one on the coaching staff.
To say the Niners are screwed staying with Kaepernick is either Niner hate talking or just a lack of knowledge of the situation. Come back and revisit in a couple weeks and your point of view will be less skewed.