AFAIK and Understand the installation or upgrade script must first check
for the running instance of the program, prompt for closing it or
close/kill it forcibly. I used to write RPM scripts and hope that must
have been done in .deb  too. The issue was last time when the upgrade
went ok and my MySQL tables were corrupted and I could not login to
MySQL server, all my apps stopped working. Some how I managed to re
install MySQL but that didnt help either and at then end some one in IRC
suggested me to run "mysql_upgrade" script and restart MySQL. It helped
and I did loose my data in all this.

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package mysql-server-5.1 5.1.37-1ubuntu5 failed to install/upgrade: subprocess 
new pre-installation script returned error exit status 1
https://bugs.launchpad.net/bugs/509736
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