The methods on this page have not been tested for upstart boot scripts. On Ubuntu 12.04, upstart boot scripts can be identified by their entries in /etc/init.d being symlinks to /lib/init/upstart-job.
There are several ways to disable a service start during boot. The ways listed here should result in the service's start during boot remaining disabled when the package containing the service is upgraded.
update-rc.d -f <service name> disablefor s in /etc/rc*.d/S*<service name>; do mv $s ${s/.d\/S/.d\/K}; donesysv-rc-conf <service name> followed by interactively changing the default symlinks. sysv-rc-conf is not installed by default. From Securing Debian Manual section "3.6.1 Disabling daemon services"
| ... the files under /etc/init.d are configuration files and should not get overwritten due to package upgrades if you have made local changes to them |
Based on that, any disabling technique that leaves at least one /etc/rc*.d/[KS]* symlink which is different from the symlinks in the upgrade package should be fine.