When I installed 0.7 I still needed to keep 0.65.2 around. Instead of uninstalling, I just renamed the Starsector folder to Starsector 0.65.2 or something and installed 0.7 in a new "Starsector" folder.
I won't guarantee that counts as a clean install, but I'm 99% sure Starsector keeps everything but its registration in the folder you tell it to install in. That means you can delete everything except for shortcuts by simply deleting the Starsector folder. If I wanted to be sure I uninstalled everything I'd use the provided uninstaller, though.