When you open up the texture with GIMP go to layer/transparency/threshold to alpha and change it to 0.
This only works with weapon textures as far as I know but its saves some time.

It also leaves unwanted artifacts on the main texture afterwards in certain cases using that method. You'd still have to go through "all the work" to decompose the original texture to grab the alpha layer to reapply it once after you're done editing the RGB image, though.