I see, it makes perfect sense to me. The secure() function was added for a reason, and in most cases it is quite useful preventing dangers such as SQL injection. So yeah, Id say its better to use html_entity_decode() on text entered by CKeditor. Removing the secure() function can negatively affect other stuff in this script.
Actually I've splited the admin.php and functions.php into multiple files for Mys v1.3.0, so are with the database tables prefix.adoptables and prefix.users since they are getting too long. Also created new folders 'classes', 'functions', 'css' and 'js' for future use, they may not be quite important now but I am sure it will help in a long run. Dont you think so?