To disable or enable a Drupal module from the command line, you will need to edit the MySQL database. First, you will select the database that you need to edit, then use the select command to see the current status of the module, then the update command to change the status of the module. So, first, you drop into MySQL command line and choose the database that your Drupal installation uses:
then use the select command to check the current status of the modules
mysql>SELECT name,status FROM system WHERE type='modulename';
That will output the current status of all of the modules. Then, you can use the update command to disable the module
mysql>UPDATE system SET status='0' WHERE name='modulename';
Or you can replace the 0 with a 1 to enable a module.
mysql>UPDATE system SET status='1' WHERE name='modulename';
(replacing modulename with the name of the module that you would like to enable or disable.)