Clearing Quicksilver clipboard history
There is already an option to clear the Quicksilver Clipboard history. Open up the Clipboard History panel, click the cog in the top right hand corner and click 'Clear'. The storage of clipboard history on disk has been removed in the latest version of the plugin, and this will no longer happen.
Finally, if you do not want the clipboard history to pick up contents from certain applications (e.g. 1Password, Keychain etc.) then open up the Quicksilver preferences, click the 'Clipboard' tab (on the left hand side) and type the names of the applications you would like Quicksilver to ignore.
You can safely delete the clipboard folder in ~/Library/Application Support/Quicksilver without affecting Quicksilver.