Basin Fill fills basins, regardless of depth. The parameter that you enter controls the slope at which the basins are filled (-1 means that Wilbur computes an appropriate slope for the image resolution). The edge of a basin is either sea level or the area that would be full of goo if the world is flooded by a viscous goo (the parameter you enter on basin fill is approximately equal to the viscosity of the good - a value of 0 means that you'll get flat-filled basins; a value of -1 means that you'll get slightly-sloping fills on the basins that allow for rivers to be correctly routed across the basin). Fun with Wilbur, Volume 5 shows how flow across basins filled with -1 look.

The way that you keep basins from getting filled is to make them not basins. Cut a small channel at the edge of the basin to let the water out.