Create a copy of webwork2.pot for the course in question. Call it something like webwork2-mycourse.pot. Modify the strings in that file.
In course.conf, set the localization to refer to that new file.
I haven't had a chance to look up the specific values for this, but that should be the idea. Of course this means that you can't modify the strings from within the course (you would need shell access), but it should allow you to create a custom localization for one course.
Danny