Interesting idea and correct me if I am wrong, but couldn't the entire map be rendered at once? Just import to Blender with KotorMax and use the .lyt file to arrange the level, then use top-down rendering techniques to make a map from it, I am almost certain I have seen a technique / tutorial somewhere for rendering a whole level to a minimap at once, I shall have to track it down.
At some point I need to re-render the K1 maps for K2 anyway so I might look into this as well ( won't be any time soon though ) as for setting up the lightmaps, I do not even know how to apply the lightmaps myself, using GMax and KOTORMax it's relatively simple to get the whole level loaded in.