I know how to uninstall a click once application using the command line or from a batch file via the Uninstall string you can find in the registry for the click once application.
rundll32.exe dfshim.dll,ShArpMaintain appname.application, Culture=neutral, PublicKeyToken=d67ac05a79f37e8a, processorArchitecture=msil
BUT, anyway to make this done silently, without a UI. Right now, when running something like the above, a window comes up asking if you want to restore or remove. I want to force a Remove and have the user not have to provide any input at all.
Not very nice but it might work: http://explore.wordpress.com/2007/12/17/clickonce-limitations/33/