Your concerns about having multiple classes with the same GUID are legitimate. Daklu's suggestion of throwing an error in such a case and adding an explicit "rename and preserve history" option sound reasonable.
This will mean that people who copy and rename the file outside of LV will get an error.
Assuming you got grades which were less than A in your CS courses, did you defend the work under the shield of the poetic license argument?
Also, personally, I'm more of a code cartoonist than a code poet, and as such, should be exempt from such stringent requirements.