How do I override the default CKEditor configuration?
To answer your question about how to modify CKEditor's config.js:

In 4.6

You need to "hack" the config.js file within CiviCRM itself (packages/ckeditor/config.js). Editing this file will modify all instances of CKEditor in CiviCRM (angular and quickform add a few additional settings related to file uploads but they do both respect that file). If you don't see your changes right away, clear your browser's cache. Note that this file will be overwritten with every upgrade.

In 4.7

4.7 adds a GUI in Display Preferences to modify plugins and button groups, and this will generate at least one config file named crm-ckeditor-default.js in your files/civicrm/persist directory (more files will be created if you click other tabs e.g. for CiviMail or CiviEvent). This file won't be overwritten during upgrades, but will be overwritten if you make changes from the GUI. There is also a new hook_civicrm_coreResourceList which you can use to specify a different config file depending on whatever logic you want like current page, current user, etc.