This has been implemented.

$conda config --help
usage: conda config [-h] [--system | --file FILE]
                    (--get KEY | --add KEY VALUE | --set KEY BOOL_VALUE | --remove KEY VALUE | --remove-key KEY)
                    [-f]

Modify configuration values in .condarc.  This is modeled after the git
config command.  Writes to the user .condarc file (/Users/aaronmeurer/.condarc) by default.

optional arguments:
  -h, --help            show this help message and exit
  --system              write to the system .condarc file
                        (/Users/aaronmeurer/anaconda/.condarc)
  --file FILE           write to the given file
  --get KEY             get the configuration value
  --add KEY VALUE       add one configuration value to a list key. The default
                        behavior is to prepend.
  --set KEY BOOL_VALUE  set a boolean key.
  --remove KEY VALUE    remove a configuration value from a list key. This
                        removes all instances of the value
  --remove-key KEY      remove a configuration key (and all its values)
  -f, --force           Write to the config file using the yaml parser. This
                        will remove any comments or structure from the file.

examples:
    conda config --get channels --system
    conda config --add channels foo

It uses a very basic parser to try to preserve the format of the config file, but if that fails, you can use --force, which uses the PyYaml module to write the config file (which destroys all structure and comments in the config file). Presently, the only shortcoming is that the two --remove commands do not support round tripping, and must be used with the --force command.

add conda config command #9

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