According to the MySQL 5.0 Reference Manual you may find an init.d script responsible for starting the service at boot.
If that's the case, consider the following:
Determine if you have an init.d script:
sudo ls -al /etc/init.d/*sql*
Take note of the name, according to the docs it should be mysql.server, it may also be symlinked as mysql.
Disable via update-rc.d
command:
If the name of the script is in fact mysql.server, then this command should disable the service:
sudo update-rc.d mysql.server disable
sudo update-rc.d mysql.server stop
In theory you can still start/stop it on demand:
sudo chmod +x /etc/init.d/mysql.server
sudo /etc/init.d/mysql.server start
sudo /etc/init.d/mysql.server stop
If you wanted to permanently remove it:
sudo chmod -x /etc/init.d/mysql.server
sudo update-rc.d mysql.server remove
sudo killall --regex .*mysql.*
sudo reboot
Hope that works for you.