This gets me half way. The repo in question ends up disabled in /etc/yum.repos.d, but is still listed in the expansion of $yum_repo_stanza.
Should I request a new feature?
Ah yes, I don't deploy RHEL5 or newer widely yet, so I don't use and didn't catch the subtle difference of $yum_repo_stanza.
I did a little more searching and found that the solution has already been added. I needed to add "enabled=0" to the Yum Options field under the Advanced section of the Repo GUI.
Here's the reference I found: http://www.redhat.com/archives/et-mgmt-tools/2008-March/msg00125.html