This is really getting misconstrued. Tactically Pete made the right choice. You don't run it on 2nd down with 1 time out and 25 seconds left in the game.
Seriously, What happens if you run it and they stop Lynch for a two yard loss? do you hurry to the line and run it again? Do you audible to a rushed pass play? Call time out and commit to passing it two times? No, you throw it, if you make it you win if it's incomplete you stop the clock and use your time out to run it twice.
The Seahawks were right to throw in the situation, the play call was bad, calling a pass was not.