This is news? Redhat (like every OS vendor I've ever dealt with) have been pushing out updates with broken assumptions for years.
In fact, this isn't even the first time they've done something similar when updating bind:
back in 2004 they released RHEL 3 update 4 and many people had precisely the same experience. Additionally, when applied, Update 4 removed the /etc/rc*.d/S*named and /etc/rc*.d/K*named and then shut named off.
As a quick glance at redhat's bugzilla shows, the first problem (the same one you experienced in this release) wasn't a schoolboy mistake on the packagers part, or a bug. It was the result of a poorly understood choice on the part of the person who originally provisioned the machine.
Rather than installing just the original bind-9.2.4, the people who had their named.conf overwritten had installed bind plus a package called caching-nameserver. It's that package that, when updated, backed up and overwrote their bind config. The "caching-nameserver" package should only be installed if you want to run a caching nameserver, because the caching-nameserver package isn't an application at all - it's simply a named.conf file.
The real bug (back in 2004) wasn't actually in Update 4's bind package. As it turns out, the package it replaced incorrectly contained a `chkconfig --del named` in its uninstall script.
Anyone without proper alerting and a good QA process found that one out the hard way. I had customers who'd gotten so blasè about performing nighttime maintenances without proper reversion testing that they scheduled nightly cronjobs that ran up2date at midnight and rebooted the production machine, Naturally, they woke up in the morning to find they'd just suffered 8 hours of downtime.
Lesson? Don't trust the vendor's QC work, don't install unnecessary packages, and make sure to QC your own work! Ask any experienced Windows admin about unintended consequences from "trusted" vendor patches...