Hi @zeh32,
What you described is the only way to do it. Well the other way is a bit technical, but basically you need to open up the browser inspector and delete the HTML element/node of the menu item and then save the settings and then it won’t come back.
I realise for some how the plugin works in this regard may seem a little unintuitive, but the reason for this is that people deactivate plugins all the time, especially for temporary measures to troubleshoot issues. So we can’t have our system permanently remove a menu item just because a plugin was deactivated, otherwise people will be constantly rebuilding their menu. So we saw this as being a lot more painful then having old menus hanging around which can be simply hidden if need be.
I hope that helps 🙂 Thank you,