Allowing Targa upload would be nice, though my personal workaround to this issue is to keep a folder of "Convert to <format>" Photoshop Droplets on my dock with various attached rulesets. That way I can just grab an image or folder of images, drop them on the droplet, and it spits out a clean folder of my converted content.
The following automation settings and droplet configuration should give you what you need (I think) provided you are using flat TGA files with only one alpha channel. I don't think the available options and settings should vary much on the PC version of Photoshop.
If you aren't using Photoshop, perhaps your software of choice offers similar automation functionality.
Obviously the folder destinations and a couple of other things could use some fine-tuning to your particular situation.