Pro version includes its own copy of a free version (or the core of a User Role Editor). So you can remove free version. The only thing that you should remember is that both versions (free and Pro) use the same place to store their settings data. So if you delete free version via WordPress Plugins Delete link, plugin will delete automatically its settings data. You will have to configure User Role Editor Pro Settings again after that.
Right decision in your case is to delete free version folder (user-role-editor) via FTP not via WordPress.