Clutch Pedal/linkage problems of the 2006 Mini Cooper S Convertible

While pulling up to a signal with the clutch pedal down, we heard a clunking sound in the center of the car. The rest of the drive, the car was difficult to shift (6 speed manual) into any gear. Took the car to an independent mechanic and the linkage was fine. They could not determine the cause of the problem. Took the car to the dealer, and was told that the throw out bearing had failed, requiring a $2300 clutch repair. That seems like a very expensive and premature failure.