Well, that's pretty much what the set light mapping on command does. You have your normal, textured level without a lightmap, and you import it. The lightmap you keep as a seperate jpeg file. The textures and the lightmap do not interfere with each other in this method, they are completely seperate. The command takes the jpeg lightmap file (NOT a COMPLETE MAP, a LIGHTMAP ONLY, which is just black and white gradients), and places it over the texture and shades it accordingly.
The only problem with this, as I stated before, is that it's only one lightmap per object. So unless you want to divide up your level and load in different pieces seperately (which I know I don't wanna do), then you can only have one jpeg file to put over the entire level. If you try to unwrap a level into one jpeg file, then there are going to be problems with detail.