They had stopped Lynch on 3rd and 2 and 3rd and 1 for no gain earlier in the game. In -and 1/2 situations where the Seahawks ran Lynch that day they were 2/4 in picking up the 1st.
The reality is, there is no "possibly". If you call timeout you must let them score, otherwise it's completely senseless. Stop them on 2nd Down and you are in the same situation time-wise as if you had not called the timeout, only with the difference that the Seahawks now would have not needed to call a pass play on 2nd or 3rd down for time reasons.
The Patriots O beat the Seahawks D by exploiting the underneath stuff. 8 yards here, 4 yards there etc. etc. That would not have worked in an end-game scenario. Patriots would have needed to create chunk plays.