I think the answer is yes. I don't know about specific geometry but you can specify how toon pro behaves for specific objects. In the attached image, I have turned off the lines for the sphere but left the lines on for the cube. To do this, select your object, select the "Effects" tab, and there should be a toon pro block of options. You can override the toon pro general scene rendering options there and substitute specific rendering options for each object.

-Kix