Add context menu item "Launch at startup". When user does so, a file will be created at ~/.config/autostart/NAME-autostart-whiskermenu.desktop The "-whiskermenu" part in filename is for Xfce4-whiskermenu-plugin to recognize that file was created by it, so that file will be removed whenever user wants, without intervening with files that were created by other programs.
Maybe this is not an appropriate addition to Xfce4-whiskermenu-plugin. Bug 12217
There is already a mechanism in Xfce for managing programs that start on launch: in the "Session and Startup" settings the tab for "Application Autostart". There you can see what programs are set to autostart; you can add, edit, or remove them as well.