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.
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.*
Hope that works for you.