As someone who lives in NC and has seen many news reports on this situation since it began, here is my take: The problem that many people had with the call to prayer was not the call to prayer itself but that it was going to be broadcast from the Duke Chapel tower. Christian leaders at Duke extended the offer of the chapel tower to Muslim leaders as a gesture of interfaith goodwill. A Muslim group had already been conducting prayer services in the chapel basement.
After the decision was reversed, the call to prayer was held on the chapel steps. This call to prayer drew a large group of Christian as well as Muslim students. This change in location seems to have calmed most of the voices in opposition.
Duke is a private, Christian-founded school with a well-known Divinity School. I am not a Duke grad, parent, employee (and certainly not a sports fan 
), so I shouldn’t have a say at all in what Duke does. However, I appreciate that the Christian and Muslim groups at Duke are committed to interfaith cooperation. I don’t agree with the protesters, but I understand why broadcasting from Duke Chapel’s tower, as opposed to other campus locations, would upset some people.