I've finally bypassed this error by stopping mysql server with :

mysqladmin -u root -p shutdown

Restart the upgrade and all is fine.

It seems that the package which do the upgrade don't have the necessary
rights to stop mysql server.

-- 
package mysql-server-5.1 5.1.37-1ubuntu5 failed to install/upgrade: subprocess 
new pre-removal script returned error exit status 1
https://bugs.launchpad.net/bugs/520335
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