How do I stop Apache from starting up automatically?
Are you sure that it is apache you are seeing running. When you do the 

ps aux|grep apache


You will see one process ( the shell process that is looking for the string apache)

A running apache server is not called apache it is called httpd, and you will see multiple instances of this (one parent daemon which in turn spawns workers). The apachectl  is reporting correctly that it is not running