Actually, it seemed clear it was a designed QB draw (I think the paper this morning said that as well). The problem I see is that even if successful, after the run you probably only get one play from the 25 yard line, a long shot at best, versus two or 3 more plays had you kept passing the ball, maybe draw a PI or holding, giving you free downs.
Just seemed to me to be pushing all your chips in the pot for one play, just not the best percentage to win, IMO. (Lets be honest, it was a long shot no matter how the Cowboys ran the last two or three plays, they probably lose anyway 98% of the time)
Of course, I also think that SF got royally screwed on the overturn of the first down at the end of the game, so poetic justice prevailed in the end.