I believe the thought is that if they get the first down they kneel out the clock, if they don't get it the 49er's would have to go 85+ yards with no timeouts and score a touchdown and 2 point conversion, then score again and get a two point conversion.
There was less than 2 minutes left when the 49ers got the ball.
Also, there is a better chance of them blocking a field goal and scoring than their is going 85+ yards on our defense. That's where Pete's head was at (and if you noticed, he was correct, they couldn't get passed mid field in 2 minutes)