Christopher Kunz have posted a suggestion to increase PEAR security.

The latest PHP worm (lupii) attacks systems that are vulnerable to a remote code execution hole in PEAR::XMLRPC (or phpxmlrpc). It can only propagate on systems whose administrators have neglected to update PHP (or PEAR) in the last 3 months. Those three months have seen 4 PHP version bumps alone in the PHP4 tree, and anyone who hasn't brought his PHP up to scale is probably a moron anyway.

Christopher suggested "pear upgrade-security" that admins will find it more easy to use. I think that "pear upgrade" is already an answer including only stable version with major security fixes. But I liked the idea of automating security upgrades even if it could make some technical problems, generally admins upgrade on a second server and test their system before upgrading on the main server. It's not interesting for them to create unstable system due to automated upgrade that they'll find more difficulties to restore later.