Escaping quotes in ckeditor breaks smarty-syntax
Adding config.entities = false; to the ckeditor-config packages/ckeditor/config.js prevent ckeditor from escaping special characters.

This avoids the issue with smarty-syntax. But I am not sure if this doesn't produce other problems by not escaping anything...
If anybody has experiences with that please post them here.

EDIT: In CiviCRM 4.7 ckeditor will be configureable. So it probably won't be necessary to patch packages/ckeditor/config.js anymore.