Here, we are concerned with the dotted black line; this represents the expected win probability of the defense given they intentionally allow a touchdown while up one point. If the current situation falls below the black dotted line, teams should intentionally allow the touchdown; if it is above, they should attempt to stop or block the field goal. Once the 49ers had the 1st-and-Goal, with the impending snap coming under the 2:40 mark, the Seahawks should have immediately attempted to allow the 49ers to score.
A couple notes:
1. Since the 1st down snap came at 2:39, the two-minute warning was effectively rendered useless - it basically gave the 49ers an extra timeout to call as the play clock wound down so they did not have to take a delay of game.
2. Since the 49ers were already inside the 10-yard line, they could not achieve another first down to continue to run the clock barring a penalty.
3. As is always the case, the 49ers would not have to score a touchdown. They could kneel down before the goal line (like Brent Celek did today) to maximize their win probability. But, trying to allow the 49ers to make the mistake by scoring the touchdown does not have a downside (well very tiny downside, the difference in probability between an 18 or 19-yard field goal and 24 or 25-yard field goal is roughly 1.5%).
Now, let's look specifically at the two situations:
1. Seahawks intentionally allow a TD: According to Brian's win probability estimates, that leaves the Seahawks with a 20-25% chance to win the game if the touchdown is allowed right away. Seattle would have over two minutes and the two-minute warning to drive down and score a touchdown. This would also be dependent on a San Francisco two-point conversion - if they fail, a Seahawks TD wins the game, if they convert, a Seahawks TD ties the game. Still, getting the ball with 2:30 left down 7 is roughly a 19% proposition to win the game.
2. Seahawks try to stop San Francisco: If San Francisco runs the ball three times before kicking the field goal, the time calculator estimates Seattle gets the ball back down two with 0:24 seconds remaining (they actually ended up with 0:26 seconds). Yes, Seattle could force a fumble (~1% probability). Yes, the 49ers could miss or have their kick blocked (< 3% chance, which decreases marginally as the 49ers approach the goal line). Taking everything into consideration, the Seahawks win probability would max out around 10-11% if they attempt to stop San Francisco:
P(FG Miss or Block) * 100% + P(Fumble) * 100% + P(FG Make) * P(Win down 2 with ~0:24 remaining)
= 3% * 100% + 1% * 100% + 96% * 7% 10.7%
In all likelihood, this is actually much closer to 4-7% as that 7% win probability given the situation is based on an average number of timeouts remaining. Either way, by intentionally allowing a touchdown, the Seahawks would at least double their chances of winning the game with very minimal downside.