Why was Harvard University chosen as the headquarters for the new regime?

I believe this was done for effect. Although if the reader is unaware that Harvard was America's first school of higher learning (university) and one of the top universities in the world, its meaning or innuendo goes unnoticed. Atwood's choice of setting a prison in the midst of a place known for its history of enlightenment is about as polar opposite a description as can be conveyed.