A CVS repository that is no longer needed can be removed as you would remove a normal directory tree. All the information CVS stores about the repository and the projects in it are stored within the repository tree, most of it in the CVSROOT subdirectory of that repository.
If you have edited the scripting files in the CVSROOT directory, they may refer to scripts stored elsewhere. Check the scripting files; if the referenced scripts are no longer needed, they can also be removed.
Once you have backed up any projects you may need to refer to later, remove the repository with rm -rf repository_root_directory.