#1: Ireland and FO would have been skewered for drafting a "project QB" with the 12th pick just like they were by many for drafting a "project QB" with the 8th pick in 2012.
#2: They had been burned by a similar "pistol" QB in Pat White (albeit, White was much smaller than Kaepernick)
#3: Sparano was in "win now" mode. Ireland does not operate in a vaccuum. He must select players based on the vision of the head coach. Since Sparano's situation was not one amenable to developing a young QB, using the 12th pick to select a QB wasn't in the conversation at the time.
I do feel had Kaepernick lasted in the 3rd round, the FO would have possibly selected him because they did appear to be high on him. But it just wasn't meant to be. We got a QB now, and hopefully he turns out to be something that fans of other teams will be posting on their forums for years to come "HOW DID WE PASS UP ON TANNEHILL!??!"