(un)Fortunately, I use The GIMP for my graphics-editing, because it’s 100% free, and available for just about every operating system under the sun. I can step you through how I added an Alpha Channel with that though.
First, after installing it, when you start it for the first time you’ll be presented with a ‘Welcome to The GIMP User Installation’ screen. Don’t panic, this is normal. GIMP supports multiple users on one computer, and it needs to do some per-user setup the first time any given user runs the program. Just click the ‘Continue’ button until the big orange-topped window goes away, and wait for The GIMP to finish loading. It takes a while the first time.
Close the ‘Tip of the Day’ box, and tell it to never come back if you want to.
Now, find this dialog box:

Using your left mouse button, drag the image you want to edit and drop it onto this window to open it. Taking the mtf1-blue.tga file as an example for this exercise, you’ll end up with this screen:

Now, go back to the Main Window (the one you dropped the file on) and click on the icon of a hand pointing at a gray box between a yellow and red box. This is the ‘select by colour’ tool, that lets you select all of the regions in an image that are a single colour. In this case, black.
When you click on the tool, a bunch of options will show up in the bottom half of that window. Turn off AntiAliasing, and set the Threshold to 0.0 first.
Now, go back to the mtf1-blue.tga window, and click anywhere that’s black. A bunch of the image should highlight.
Now, go to the one window you haven’t touched yet, the Layers, Channels, Paths, … window. Right-click on the image of the Background layer, and click on “Add Layer Mask” if it’s available. If it’s not available (grayed out) click on “Add Alpha Channel” first, then go into the right-click menu again and the option will become available. When asked what to Initialize the Layer Mask to, pick White (Full Opacity) for now. The Layer Mask will be the ‘active layer’ now, as evidenced by the black border around the actual image, and the white border around the new Layer Mask. (Trust me, you’ll notice it more when you come back to this window in a moment.)
Now, go back to the image mtf1-blue.tga window, and right-click again. Under the Edit menu, pick ‘Fill with FG Color’ to fill the selected areas of the image with black in the active layer. Since the Layer Mask is active, this fills in the ‘solid black’ areas in the image that we selected earlier with Black, marking them to be set transparent in a moment.
Press Ctrl+Shift+A to unselect everything, since we’re done with that. Next, press Shift+= three or four times to zoom into the image, go pick the ‘Pencil’ tool, and click on the little left-and-down arrow in the upper-right corner of the Colour Selector to switch the foreground and background colours. We want to draw with white for a moment, not black.
Going back to the mtf1-blue.tga window, you should see something like this:

What we’re going to do now is remove the ‘tiny flecks’ of transparency (the checkboard gray pattern, like PhotoShop uses) from the image, as they don’t tend to show up well in-game, nor does q3map2 handle them well when casting shadows. So, see those two little flecks by the big long diagonal slash on the left half of the window? Move the mouse over them until the highlighted circle (that’s your brush) covers them, without covering any of the diagonal slash itself. Then left-click lightly. The circle should vanish for a moment, and the two flecks of transparencyshould fill in with black again as well.
Continue cleaning up any spots of transparency that don’t make sense, like this area:

When you’re done, it should look more like this:

Now, go to the Layers window again, and right-click on the Layer Mask. Select ‘Apply Layer Mask’ and you’re almost done.
Go back to the mtf1-blue.tga window, right-click, under File select Save as… then save the image as whatever you want, just as long as you make sure it ends in .tga and not .jpeg, otherwise you’ll lose the transparency information. When given a window of options to use for the ‘Save as TGA’ filetype, make sure RLE Compression is unchecked and Origin at bottom left has to be checked before clicking OK.
Viola, you’re done. Press Ctrl+Q to quit The GIMP.
Oh, and here’s the new .tga file if you don’t want to trudge through the above:
http://wolfwings.us/mtf1-blue.tga