I'd try this if I were tasked with the job. Duplicate your basic image into two layers. Hide the bottom one for now. On the top layer, apply a mask and invert it. This will make what is white on the image
invisible (or transparent) while keeping the black line art visible. This will also retain the smooth edges of the black line art.
Hide this layer, and re-enable the previously hidden untouched layer. Do your wand-thing, except after selecting an area expand the selection by a pixel or two. Fill and shade as desired. Don't worry about colouring over the lines. Once you're done, un-hide the masked copy of the line art, and make sure it's on top of your newly colored version. You ought to have some nice, crisp lines over your coloring.
I'd give you photoshop-spesific instructions, but despite owning Photoshop I continue to use Fireworks for my editing, and would have a hard time making a mask in Photoshop myself.