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As an organizational question, wouldn't it make more sense for methods needing docstrings to be in the library rather than the executable (the executable isn't part of the library which means a user isn't going to import it and actually call those functions).
You do, however, want to document the shell usage and possibly other aspects of the executable. Sphinx has an extension that will grab program output (which could be used with morpho --help to get the usage out of argparse). There may be other sphinx extensions for executables which do more what you're looking for but you'd need to look through the sphinx documentation to decide what works best in this case.
Doc strings have been added to the morpho executable, but readthedocs is only showing docstrings from code inside the morpho folder.
http://morpho.readthedocs.io/en/latest/
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