Is it possible to use drush to save a theme setting?
Drush does not have any facilities for manipulating elements of arrays in the variable table; however, you can use drush php-eval to call variable_get() variable_set(), and include a bit of php to manipulate the json yourself.

It would also be pretty easy to make your own Drush command to manipulate the items you'd like to set regularly.  See the drushify tool for a fast way to get started.