From press reports it appears that Toyota has known since 2007 that it has a low-incidence problem with full-on acceleration, presumably caused by sticky accelerators but not conclusively linked to a single mechanical cause.
I have no experience with Toyota engine computers, but if they are like European ones they receive input from the brake pedal switch as well as accelerator position via the throttle position sensor and engine RPMs via the crankshaft sensor. The software is contained in flash memory that can be reprogrammed by the dealer.
Thus the problem can be dealt with positively — no matter what the cause — by reprogramming the computer to override the throttle input and shut off gasoline to the injectors (or limit it to idle levels) when the brake pedal is depressed for more than an instant. Even if there is a bug somewhere else in the software this override can be accomplished in a way that has priority over other instructions. This might impair drivability under some race car scenarios but would be much superior to the current state of fear that is being imposed on Toyota drivers.
At the same time, software diagnostics should be added to track discrepancies between throttle position and engine RPMs, to ensure that the cause of the problem is indeed mechanical at the accelerator pedal (or a driver-induced problem) rather than a fault in the computer or other engine component.
This solution seems so obvious that there must be something I am missing!