This page does not apply to upstart systems.

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> disable
for s in /etc/rc*.d/S*<service name>; do mv $s ${s/.d\/S/.d\/K}; done
sysv-rc-conf <service name> followed by interactively changing the default symlinks. sysv-rc-conf is not installed by default.

Reference

From Securing Debian Manual section "3.6.1 Disabling daemon services"

Quote:

... 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.