I didnt see the game but just looking at the stats they have Kaepernick attempting 7 passes. Dont know if Alex Smith was hurt or benched for throwing 3 int's.
Actually after reading some articles it sounds like Harbaugh just inserts Kaepernick at random times. Seems 49er fans are not too happy about it. I would have to agree with them, you dont want to mess around with the QB position.