another way to do it might be to use the gimp and perl-fu. Your program can call gimp commands programmatically and ought to be able to fill a region if you can give it a point inside each county. Though SVG or some postscript or pdf thing might look prettier.

Just a wild guess but you might be able to even make a PDF template of the map and then replace colors at appropriate places in the program, if you are feeling adventurous.