I use a baby wipe on the foot bed, IYKWIM. It seems to do the trick. If the other alternative is to throw them away, it might be worth trying to wash them. I've done it before for some of dh's (gagging emoticon).
Get your normal washing powder and an old toothbrush. Make a solution of washing powder and water, shuffle it about until it goes bubbly, then use the toothbrush to scrub the stinky parts. Rinse well, then let them dry out in the sun. Hope it works!