what kind of marks???
not quite sure what kind of marks you would get from pins??? are they dirty???
pin holes do disappear when the quilt is quilted, bound and washed.
but if the pins are leaving some sort of...stain??? i would remove a guilty pin-and spot clean immediately to see if its coming out---and i would clean the pins...i would not leave in for any length of time any pin or any other (tool) that was soiling my quilt