There are a couple of things to consider here:
First, Blender's viewer is currently broken for associated alpha, which is the default format the renderer produces. That means that the viewer won't show the pixels that are both luminous and fully transparent (alpha zero, RGB not zero) from an image with associated alpha.
If you're going to composite that effect using Blender's compositor, just try an alpha over on a colour to judge whether your image transparency is correct instead of relying on the RGBA view of Blender's image viewer.
Also, you have to understand the kind of effect you're tying to achieve: This is a lighting effect that you want to be added to a background.
As easy as it sounds, adding that luminous element can be done via a simple add. You don't even need an alpha channel (because there is no occlussion), you can just add the RGB plate to the background and it look ok.
If you want to produce an RGBA image that can be composited with an alpha over anyway, keep in mind the following:
- ONLY associated alpha (often called pre multiplied) allows the compositing of pixels that are luminous and transparent, so choose a file format that supports associated alpha (the most common for visual effects is EXR)
- It's impossible to produce that kind of alpha blending with unassociated alpha, so formats like PNG are completely ruled out.
- Image editing programs like Photoshop and GIMP work internally with unassociated alpha, so they are not suitable for compositing that kind of effects with alpha blending. You need to cheat and use an RGB only image with an addition instead (those programs are also likely to destroy the RGB information of every pixel with alpha=0, so be careful).