I think I know the answer:
1. Seattle was playing their base 4-3 defense when facing 2 WR, and 2 TE (VD and Delanie) in the spread. Please correct me if I am wrong, but it didn't look like they were playing nickel. That defense made it favorable for the 49ers to pass the ball, which they did.
2. When Gore did run the ball, he wasn't being that successful. In the end, less than 3 yards a carry. Some of their trick run plays, though, were netting good yardage.
I would also like to note that in their last meeting, Gore was not that successful running the ball. Yes, he had those 2 long TD runs, but outside of that, he was getting minimal yardage. You can't sustain drives when you consistently are running for 1-2 yards, and you can't count on hitting on a 80 yard run each game.
I think the 49ers made the right call to pass the ball (although I was surprised that they didn't call at least a few more run plays to keep the defense honest). In the second half, the 49ers did try to run the ball more, mainly due to bad field position, and the end result was fewer points scored by the offense.