All of your settings will remain on your site if you remove or uninstall Link Whisper. Also, all of the link data, Auto Link Rules, Target Keywords, and URL Changer rules will remain on the site.
The only way to remove all of this data when uninstalling the plugin is to affirmatively turn on the option to delete all Link Whisper data. If this option is active, then uninstalling Link Whisper will delete all of its setting and rule data on your site.