Finally I've found a workaround solution for my problem and I want to share it here, just in case someone else wanna have custom css in his/her courses, too.
What I did was to activate the "Legacy Course Files", i.e. the old file management system from moodle 1.9. This plugin allows you to upload files to a specific course, that have a fixed url. The fixed url is important for embedding the custom .css into the html (without having root access to the webserver)
With the new file system from Moodle 2.0 the uploaded files do not have a fixed url anymore (as far as i know). The problem there is, if you upload a .css file, that has the same name than an already existing one, the old does not get replaced. Instead there is a new (database) entry generated that has a different url. Thus the html sites still reference the old .css file and do not get updated.
With the legacy course files you can delete the old .css, reupload the new .css file under the same name and on this way assure, that all html sites, that referenced the old .css file, now use the new one and thus get updated.
I know this is just a workaround and the legacy course files are somewhat "deprecated" in Moodle 2.0. But I've found no other solution to give my teachers the chance to style their courses to their liking in a comfortable way (and without root access to the webserver).
Cheers,
Philipp