What program can bake transparent light maps?
Not sure what sort of lightmaps are produced by blender. Perhaps if you can get it to render a non-transparent lightmap (for example one that has all the colours you want but on a black background), you could then use a program to remove all of the black. I believe GIMP and Photoshop both have a colour to alpha tool. Be sure to pick a background colour that will not be the same colour as any of the lights.