I've had good service using a whet stone...a very fine grain one... with LONG strokes in the direxion of fork movement. Do this VERY LIGHTLY, almost NO PRESSURE against the fork tube. Just remove any "lip" the pit may have in this manner, then fine finish with 600 grit cloth backed abrasive soaked in oil... or even jeweler's rouge... A small depression where the pit is won't usually cause a leak... What really causes leaking is rough edges of pits ... unless they are really big ones...
When slipping the tubes into new seals, have the tubes coated with fork oil.... be sure they are clean of all grit too...
JR