This issue started with the Seahawks getting too cute with the clock. You are down 4 points. You certainly don't need to rush after the first down run but you also shouldn't run the clock all the way down because with only one timeout left it limits your options a bit on a potential 3rd or 4th down and you have to remember you are still down by 4. If you are down by 3 and a field goal ties it, then letting the clock run down more makes more sense.
Pretty simple what you do. You keep your big formation in there, which was in there on 1st down. With about 39 seconds left you run the second down play with Lynch. If you get stuffed on the second down, you quickly get everyone back in formation and run another run play with Lynch or Wilson with like 20 seconds left. If you get stuffed again then you immediately call your last Timeout and you run the 4th down play which could be anything.
Under this scenario, if you score on 2nd down you are now up 3 with like 35 seconds left. You do kick deep and the Pats get the ball at about their own 20 with about 35 seconds left and 2 TO's. Could Brady drive down the field and tie it? Possibly, but worst case you are going to overtime.
I really believe the Seahawks put their 3 WR set out there on second down thinking the Pats would see that and immediately call a Timeout. They didn't and Seattle didn't really know what to do with the play. So they kept letting the clock run and went with the pass.
Letting the clock run makes perfect sense. Giving NE the ball with 45 seconds and only needing a FG to tie is about a 50-50 possibility of OT. Shoot, Seattle managed to get a TD in less time at the end of the 1st half. Ideally Seattle would have scored with under 15 seconds left on the clock, which would have meant waiting until 3rd down to score. So how do you do that? You run a play on 2nd down with about 40 seconds left, a play not intending to score like a QB sneak but intentionally stopping just short of the goal line. Then let the clock run down to about 15-20 seconds, handing the ball to Lynch. If he doesn't score, burn you last time out and run your last play, probably another run by Lynch. Even if Seattle would have converted that TD instead of throwing an INT, it would have given about 30 seconds and Brady a shot at tying the game.