According to what I understand about WP Rules for plugins, the plugin available on WP is supposed to be fully functional code. Putting items to be checked within the settings and displaying a "Warning" that this function isn't available in the free version would be getting very close to, if not crossing the line of what is a "fully functional" plugin.
You place a link to your website and name of your plugin on the home page and you do not have a setting that allows the removal of that footer link. According to WP rules, if you have such a link and name of your plugin it is supposed to be defaulted to "OFF" and the option for the admin to turn it on.
This plugin violates WP rules as I understand them. Please correct these things. If you don't want people to have the functionality in your free version, remove it. You are allowed to put the differences between the free and paid version in your WP description. I see a lot of developers do that.
But, you cannot (according to what I read in the rules) force your links into the header or footer of a website without allowing people to choose to put it there.