Hi religionstudent,
I have a bunch of friends at Duke's Religious Studies Dept and, as you mentioned, they tell me that there is a lot of interaction between the two schools. I know Duke people in early Christianity and in New Testament who have Bart Ehrman (from UNC) on their committee, for example. I don't know your subfield, but it doesn't seem like you can really make a wrong decision here. If you've got big names at UNC and you think you'd get along with them, I'd go for it. Or if you think you'd be happier with the program setup at Duke, at least you'd still get to work with the UNC folks. If Duke doesn't have people you'd want to work with primarily, if it were me, I'd go with UNC. But if everything were equal in my mind (the quality and approachability of the profs, the program setups, etc.), I would go to Duke for the name. That's just me.