In several articles and forums I see people telling the way of removing the init-script on a Debian system would be:

update-rc.d -f init-script-name remove

The more appropiate way is to disable the init-script from running at boottime:

update-rc.d init-script-name stop levels .

In this way you prevent that in case you upgrade the package a new init-script will be created with the defaults.
If the init-script is written with the defaults the init-script might start the process again at boot-up.
If you disabled the init-script from running at boottime the init-script would not be recreated or overwritten with the init-script in the update.