As much as I understand your point, there's some validity to Murf's statement. Manningham isn't a possession WR, he's a 4 targets a game, lucky to get 2 catches deep ball WR. Belicheat obviously doens't know what route Manningham is going to run (unless he's cheating and stealing plays again) but it's safe to say that based on film, Manningham isn't running a lot drag routes across the middle. That means he's going up the sidelines. If your strategy at the end of the game with the lead is making somebody beat you deep with their best deep threat, well, that's not good coaching. If Belicheat was on tape saying "Don't let anybody get behind you" or "we can't give up the deep ball" then the onus is off him and on the team. But saying "Make them go to Manningham" translates to "cut off every short route and make them beat us deep, even though they clearly need big plays". 
I would argue that Nicks is, without doubt, clearly a more dangerous deep threat than Manningham - a threat that had been the most dangerous and explosive WR in the playoffs.
I'm no Patriots fan by any means, but I don't see how "Make them go to Manningham" was a bad strategic move....especially when taking into account that a little earlier, he had blown a big gain by losing sight of how close he was to the sidelines.