Leah Day says she puts her heel on a book and then uses the front of her foot and toes to press on the pedal. Keeps the angle of her foot less acute and could help reduce some of the pain. I never tried it myself.
By the way, how do you train yourself to use your left foot on the pedal so you can use your right knee on the lifter? I was having a terrible time trying to do it the other day. Just practice?