A couple of thoughts that may or may not actually answer your question:
1. I don't actually use the WeBWorK classes page for general access to WeBWorK. Instead, I have a separate page in the webserver's htdocs directory that points to the active courses that I want to have "obvious" to users. There are a couple of ways to do this, from just having a list of links to setting up a selector that allows users to pick a class from a list (e.g., the homework selector at
2. Whether or not you're doing that, you can hide courses so that they don't show up on the /webwork2/ page, by putting a file called "hide_directory" in the course directory. I do this routinely with the admin course and my template and sample courses.