if you are using Apache httpd.conf, you have to disable it from httpd.conf.
If native configuration is used for vhost configuration, we will investigate.
You may need to stop Apache from command line if the plugin cannot stop it.
For the php processes, you should check who are parent processes for those "/usr/bin/php" processes.
Never run PHP as CGI with LiteSpeed. It wont work. If you want to avoid persistent PHP processes, change configuration of lsphp5 external app, exit after process one request. but I do not think anyone should do that, it only hurts performance.