If the quills are causing problems, switch to a track type pedal like the MKS "Sylvan:"


The Sylvan is a shameless copy of the Campagnolo track pedal and quite affordable. They're are also available in a slightly wider, quilless "touring" version for about the same price.

If you're on the cheap you can simply saw off the quills on your present pedals to convert them to "track" style.