Shaun's first half was no different than any of his other performances -- generally consistent, made the easy throws, couldn't make the tough throw, occasionally made the clutch throw (4th-down pass to Vernon). Played safe and stodgy, but at least good enough to keep the Niners in the game. In other words, he wasn't the train-wreck that the lop-sided score made it out to be.
This ATL loss was due to the defense succumbing to an extremely hot QB. Giving up two huge passing plays in the first quarter would kill any conservative team like the 49ers. The D's risky gambling style finally backfired against a QB who played absolutely wonderfully in the first half, just making perfect throws.
Example -- the 90-yard throw to Roddy White. Niners down 14-10 and the Falcons had a 3rd-down on their own 10, Ryan made an absolutely perfect throw to White on a short out pattern. Clements had tight coverage, saw the throw coming and 8-of-10-times he bats down that pass. But Ryan's location was pin-point perfect and Nate had no chance.
A less-risky CB might have simply laid back and made the tackle, but Nate (as well as the entire defense) is a risk-taker. And it backfired this time against a QB who played extremely well.
So c'est la vie. Moral of the story is that the Niners' defense (especially the secondary) will have to become more conservative, stick with a bend-but-don't-break strategy. I'm guessing they feel pressure to compensate for the offense's lack of scoring, but that's not how they're going to win games. They're going to win games by being patient, keeping guys in front of them, being willing to give up FGs rather than TDs, and hoping for 16-13 victories.