If they had called it, the 49ers would've gotten 4 more plays. Defensive holding or a pass interference is an automatic first down.
Or they could have called offsetting penalties and replayed 4th down. I'd say the refs were pretty consistent in 'letting them play' the whole game. You can't really expect them to change that at the end of the game and say they are going to decide the Super Bowl.
I think the Ed Reed offsides should have been called on the 2-pt conversion. Also I've seen rumblings that the competition committee will almost surely adopt a rule to put time back on the clock when there's a holding call on a safety.