No, Alex Smith is definitely a shaky quarterback. He does what Harbaugh wants him to do pretty well, but he isn't someone who will light it up. Of course, he's not Tebow level crappy, either. I think he's good enough to be a starter, especially in the right offense.
Really, yesterday he played the same way he played against the Saints and the same way he has played all season and for most of his career. There were about 2 and a half quarters against the Saints where the 49ers offense did absolutely nothing, too.
They lost yesterday because they lost the turnover battle that they usually win (they dropped two interceptions and had an overeager backup up punt/kick returner) and they didn't win the field position game they usually win (mostly because of the turnovers but also because their punter didn't do quite as well as usual). The defense and running game was actually better than usual, and Smith was average for him (the big plays to Davis made up for the rest of the stinkiness). Add it up and the Giants are going to the Super Bowl.