You can remove plug-ins completely by deleting the plug-in files
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Safari stores its plug-in files in one of two locations. The first location is /Library/Internet Plug-Ins/. This location contains plug-ins that are available to all users of your Mac and is where you will find most plug-ins. The second location is your home directory’s Library folder at ~/Library/Internet Plug-ins/. The tilde (~) in the pathname is a shortcut for your user account name.
To remove a plug-in, use the Finder to go to the appropriate location and drag the file whose name matches the description entry in the Installed Plug-ins page to the Trash.
After you remove a plug-in by moving it to the Trash or another folder, you’ll need to restart Safari for the change to take effect.