First of all, as a general update, all involved are doing well. Everyone's been out of the hospital for more than a week and the climber who fell is walking around and recovering nicely.
The belayer has given me the go-ahead to post some details of the accident so others can learn. The belayer was not using an autoblock belay to belay the second. What happened was this: The belayer got to the top of the second pitch and anchored into the tree with the rope. She realized that the tree was about ten feet to the right of the route, and having run out the last bit of the pitch, didn't want the second to swing if he fell near the top. So, she tied off to the tree long and walked over to belay directly above the pitch. To make sure that she didn't get yanked off the ledge if the second fell, she put in a "directional" nut in a horizontal crack around five feet above the ledge (i.e., head height), and redirected the rope from her belay device, through the horizontal nut, down to the second. The second fell and the nut popped. The belayer had been breaking "down" (i.e., with the break end of the rope on the bottom and the climber end of the rope on top in the belay device), but when the nut popped, the rope to the second suddenly pulled straight down, rendering her "downwards" breaking motion worthless. (Does that make sense?) The second was quite heavy, and once he got going, the belayer was unable to get control of the rope.
The takeaway from this accident is that we must always keep in mind the importance of preparing for the direction of pull when belaying, and setting up the system to make sure that the direction of pull is constant. The belayer was prepared to be pulled up into the nut, but once the nut popped, she had no chance to move her break hand to proper brake for a downward pull. Personally, I always prefer to belay directly off my harness, ready for a downward pull (and and "upward" break) when on a ledge.