File responsible for the MySQL version is /var/cpanel/cpanel.config
Open it, find the variable mysql-version and edit the value to read mysql-version=5.1
And finally run
# /scripts/mysqlup
This should upgrade your MySQL version to MySQL 5.1. For better understanding of the process behind, /scripts/mysqlup, go through the code and browse the URL http://httpupdate.cpanel.net/mysqlinstall/
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