My opinion is that the other big problem with two foot driving is when in a panic situation you're likely to stomp on both of them.
Shortly after switching from a manual car to the Prius, I almost ran over a person on a morning jog who crossed a residential street. The brake pedal on the Prius (and most automatics for that matter) protrudes far above the accelerator (I.e. moving your right foot to the brake requires you to lift your foot or bend your knee). On this particular incident, the sole of my dress shoe got caught behind the edge of the brake pedal, because in trying to move my foot to the left as quickly as possible, I didn't bend my knee quickly enough. I could not brake in time.
I concluded that operating two pedals with the right leg/foot when you have a perfectly healthy left leg is wasteful, an unfortunate relic of the manual transmission past, and unsafe. Since then I have been driving with both feet.
As soon as you retrain yourself that the right foot is for accelerating and the left foot is for decelerating, then your concern goes away. In addition, the Prius, and most other newer cars, have brake override, so even if you were to push both, the ECM will disregard the accelerator input. It is yet to be confirmed if the Model S has brake override - I intend to test it. If every new driver was trained from the beginning to use both feet, there would no issue either.
In my opinion, though, the safest approach of all would be to just have a single pedal, with computer controlled application of friction brakes if the pedal input exceeds regenerative braking capability.