Hmm, the uninstaller removes everything when I test it on both my desktop and laptop. What OS are you running? Is it just the start menu shortcuts, or is there anything left at program files\Darwinbots3? If you go to control panel->Add remove programs is there an entry for Darwinbots3?
Right now you can just grab the SVN whole and put it on disk, but eventually there are going to be tags and branches that we won't most people to sync to. Plus not everyone will want to have to use SVN to get the source. An installer is always nice. Plus, even if you don't run the source installer you'll have to have run the DB3 installer so the registry keys exist.