Thank you for your complete bug report.
It would seem this can be fixed in the upstart job with a line like 'kill
timeout 300'. From man 5 init:
| kill timeout INTERVAL
| Specifies the interval between sending the job's main process
| the SIGTERM and SIGKILL signals when stopping the running job.
** Changed in: mysql-dfsg-5.1 (Ubuntu)
Importance: Undecided => High
** Changed in: mysql-dfsg-5.1 (Ubuntu)
Status: New => Triaged
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MySQL upstart stop job does not cleanly shutdown mysql
https://bugs.launchpad.net/bugs/620441
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