If you want to edit .TGA files, then download the 7.1 update for adobe photoshop 7, the link is here for pc and here for mac
If you're editing .bmp's, you don't need to do that
Now open up the file and go to the channels tab (should be on a floating pallete)
Go down to the Alpha channel and click it. Everything turns Black and White
If it's black, it doesn't show up on the skin. If it's part of a team colour section, then this doesn't count and it will show up anyway, you can tell if it's team colour cos its usually slightly gradiented. If what you're trying to delete has team colour on it, give up
Now, black out the area where the weapon is on the skin and import the skin back into the game (after converting it to .blp of course)