If polyurethane is not food safe, why is it used on dining tables?
According to FDA regulations, the typical clear wood finishes that dry to a hard film, including polyurethane, are considered food safe.  Wait to use the surface until the finish is completely dried, and clean it before allowing food contact.

Polyurethane is a fine choice to use on a counter, as long as you don't use the counter as a cutting board.  If you do cut directly on the polyurethane surface it will be damaged.  Mineral oil would be a good finish for a wood counter that is to be used as a cutting board, but you have to renew the mineral oil fairly often.  

As you've found, shellac is not an appropriate choice for an area that will get wet frequently.  However, you will not have any problem applying polyurethane over the shellac.