I am having a similar problem.
Actually, I have seen in other threads that there is a way to disable to javascript filter for the entire site (although I can't seem to find this in the admin area), but a better solution would be for an administrator to be able to grant javascript rights to course creators and/or teachers.
I tried to disable it through code by returning the same text that was passed in in the "cleanAttributes" function in /moodle/lib/weblib.php, but it is still changing my javascript. The reason I need it is for
AJAX. We have mixed some of our old site into moodle, and I want those pages from our old site to show up in the middle column without refreshing the entire page.
Any ideas would be very helpful.
Regards,
Robert Piercy