You know, it doesn't make sense in hindsight, but every coach should tell you play defense to the end, and stop a score (I'm talking about that whole drive, not when it became obvious that they had to let them score and get off the field). I mean, why not let them score on a quick 80 yarder and take the ball with two timeouts and 3 minutes left, by your logic? Rhetorical as that may be, the fact is no points are guaranteed. You can't assume Brady will drive the distance and score a TD after the Giants score early, again there is no guarantee. It didn't work for the Packers in SB XXXII letting Davis score a TD with 1:58 left. Though the Colts never let the Saints score per-say, it didn't work for Manning when he had over 5 minutes left at the end of that SB. In summation, I say play your best defense for as long as possible.
Another point, you can't force a team to score a TD when they are running plays to control the clock and specifically not score quick.