you can disable the warnings by setting the Moodle debugging level to "Normal".
Or, if you want to leave Moodle's debugging at "Developer", you can add the following line at line 1082 in "course/lib.php"
- $mod[$seq] = new stdClass();
However, you will probably get more PHP warnings because basically the version of Moodle you are using is old and not intended for the version of PHP that is running on your server.
You will fix many problems if you upgrade to a more recent version of Moodle.
When you upgrade your site, you will need to upgrade to Moodle 2.2 first, and then upgrade to the most recent stable version of Moodle - currently Moodle 2.6.