QB,

Agree that you don't necessarily need to be clipped in but that you may need a stiffer platform.

I'd also recommend trying inserts. Specialized makes some that will help spread the pressure on the ball of your foot (metatarsal button). You can try that. Friend of mine had the same issue and tried the inserts but found the Merrell inserts actually are working for her. However, she also compensates a bit by moving her foot a tad so that the focus of pressure isn't on that spot.

Either way, this is a common issue amongst cyclists and runners.