I have an old droid with an SD card inside, which I can access from the USB cable. I was wondering if I could use a tool like unetbootin to install the desktop version of android without damaging the mobile's android.
Unetbootin will not overwrite files unless they have the exact name as a file or folder already on the file system. You should mount the ISO before running unetbootin to make sure none of the files currently on the SD card have the same name as the files on the ISO. This way you will be sure nothing will be overwritten.
Unetbootin will, however, install SYSLINUX which will overwrite any boot loaders on the SD card.