The conspiracy theory about Big East refs sticking it to SU is extremely shaky because basketball refs are not affiliated with any conferences. Referees are basically independent contractors and work as many games as they can. This means they'll typically work the same few conferences due to travel reasons, but there is no such thing as a Big East basketball ref. For example, Ray Natili has worked Northeastern at Towson, Rutgers at USF, Troy at North Texas and Appalachian St. at Miami during the last week. Only one of those games included Big East teams.
I was at the game and Mike Roberts was the ref who drew most of Boeheim's ire, especially during the second half. The two of them were going back and forth a lot.