It's very hard to troubleshoot something like this remotely, as I'm not familiar with how the RPM package was built and configured. I use yum a lot (support 30+ CentOS and RHEL servers), but I don't use yum to maintain Roundcube, it's much simpler and easier to maintain when it's installed from tarball.
But a 500 error sounds like a database problem. I'm wondering if an update was loaded that requires a change in the database schema, but yum doesn't do the DB update part? Does your yum installation include the installer directory? If so, enable the installer in the main.inc.php file, then open the installer in a browser and run the database schema check.
Also, check the permissions on the logs directories, they need to be writable by the apache user. The non-yum roundcube logs are kept in a logs directory inside the roundcubemail directory.