Sorry to know about the freak injury.
For cycling, shoes with relatively hard sole is recommended, so that the pressure from the pedal is distributed over the entire sole. I think the shoe is not the issue in your case.
The pedal might be the culprit, I presume it is small in size. It happens to me too, when I ride my old bike with spiked steel pedals.
Eventhough, I initally sniggered at the huge platform pedals that comes with Trek, they are actually comfortable and confidence boosting.
Changing pedal might help