New England didn't call a timeout after the first down carry because they were not going to even contest a rushing attempt. If Lynch had been given the ball on second down, the line would have allowed Lynch to score. The timeout is worth more than the time to New England at that point.

Think about it, why was New England in a 4-3 look 2nd and goal from the 1-yard line? They were playing pass all the way because they didn't want anything other than a TD/turnover/incompletion. Had the Seahawks scored a TD, the Pats would have had the ball with 24ish seconds left and all three timeouts, needing only a FG to tie.