I don't think FS2 actually uses any registry thing for installation, at the very least, FSO doesn't. As such, I haven't actually *installed* FreeSpace over the past like, six reformats.
All I do is copy and past the entire game folder from the old HDD onto the new one and the game runs just fine.
So, if you don't want to redownload everything, you can just copy and paste the folder. Probably won't integrate with Steam's UI anymore, but I'm not sure if Steam's UI even integrates with FSO launched via the launcher.
If you want to pre-download the files for the MediaVPs, then I think a manual installation is your only option. It's really easy though (basically dragging and dropping the contents of a *.rar file into a folder).