Disabling upstart jobs

Have you used rcconf/chkconfig to disable services from booting up? have you even checked the correct rc directory to see if it starts with a "K" vs a "S" and services are still booting up? You should probably check if the service/daemon was converted to an upstart job.

System upstart jobs are found in /etc/init/

the simplest way to disable the service from starting is to rename it. So, for example the service "smbd" would be stopped from starting like this:

mv /etc/init/smbd.conf /etc/init/smbd.conf.disabled

This way, you can keep the original configuration file and it will be plainly noticed that its "disabled"