Ultimately, I believe what Johan stated previously is correct. If your
mysql daemon is not stopping when you tell it to shutdown, then you
should be concerned.

I've pushed a branch up now that raises kill timeout to 300 seconds.

5 minutes should be long enough for most databases to finish flushing.
Any longer and the system reboot/halt will be delayed unacceptably. I'm
thinking about what happens when a UPS dies and the sysadmin tries to
shut down the server. kill -9 is still less violent than a total system
power off!.

I'm also starting a discussion with our documentation team about
recommending InnoDB as the safer table type, and I've opened a new bug
report to suggest that InnoDB be the default table_type:

https://bugs.launchpad.net/ubuntu/+source/mysql-5.1/+bug/633364

-- 
MySQL upstart stop job does not cleanly shutdown mysql
https://bugs.launchpad.net/bugs/620441
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