Looking at https://bugs.launchpad.net/ubuntu/+source/mysql-dfsg-5.1/+bug/574557 
,
could you try

    start mysql

to see if that'll kick your upgrade process?

Also, I still would like to see the output of
    ps -ef
(before and after you do 'start mysql')

-- 
package mysql-server-5.1 5.1.41-3ubuntu12.3 failed to install/upgrade: 
subprocess new pre-installation script returned error exit status 1
https://bugs.launchpad.net/bugs/627723
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