Private betas are no longer locked down like they once used to be (they're accessible at any time from Area 51), so removing them entirely isn't necessary. In fact, they're deliberately included in the site switcher to increase their discoverability. The site switcher is newer than the full site list on stackexchange.com, so if anything, we should reconsider hiding them there.
These two course-specific sites are experimental. At the moment we don't have a site state for "fully private" and special-casing individual sites in our code is just going to turn into an unmaintainable mess very quickly, so we aren't planning to make any decisions about how sites like those are handled until we know how successful those experiments turn out to be.