Yep, that shouldn't be a problem. Just put your themes wherever, and then make a symbolic link to the Themes folder so ThemeChanger doesn't get confused. (A Mac OS alias might work too, but I can guarantee a symlink will.) To create the link, go to the Terminal and type this:

ln -s "/Volumes/mydisk/path/to/actual/Themes/folder" "/Library/Themes"

So if you put your themes in a folder called "Themes" on a disk called "GUI Stuff", it'd be:

ln -s "/Volumes/GUI Stuff/Themes" "/Library/Themes"

Hope that helps.