I don't think there is any command line utility to add a single user to the course. If you have a script to import a classlist into the course that should let you add users. I'm not seeing an import_classlist script in the WeBWorK bin directory, so I'm not sure what that script is doing.
Another option is to manually add the user to the appropriate WeBWorK database tables, but that's probably as hard as creating a new course and deleting the old one.
WeBWorK Main Forum
Adding Instructor to a course.
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