What should they have done differently?
Um ... a ton of stuff. I assure you this wasn't run like anything you witnessed at Gampel or the XL Center. The school was unprepared for such a large and rowdy crowd. They wanted to create this type of atmosphere and were ignorant of what was likely to happen.
First, they did not do an adequate job conducting searches before the game. You had clearly intoxicated students allowed to enter and tons of excess alcohol in the stands.
Second, you had students sections rows from the visiting teams bench and visiting fan section.
They had no "event management staff" or police in the area where you knew problems were going to arise.
This was a league Championship event - not a Bryant home game - and NEC officials allowed this environment to happen, knowing there were previous incidents in the QF game vs. CCSU and Semifinals vs. Mount St. Mary's
When adults don't act like adults - this is what happens.