Strange, I always thought the Confederates were Americans. They thought of themselves as such, and counted the first President George and Tommy J as their own. (They were from Virginia).
I'm sure if it had been a Green and Black flag of pan Arabism, it would not have been a problem in the eyes of the faculty and staff.
In fact the Confederates wrote a constitution for their country ~ I do not believe they were as confused about what they were doing as are a number of moderns.