It is not unusual when monies are misappropriated that charges aren't filed. Sometimes organizations don't want that info getting out and they fire and find some sort of settlement with the folks that stole the money. I know of a NJ law firm believe it or not that their CFO was stealing for years and they didn't want the bad press out there especially because they do a lot of criminal white collar trials and they didn't want the bad press.
But in a University setting, to me it is more unusual because although the bad press hurts, people generally understand this stuff can happen. Nyre's need for more oversight is not unusual at all and seems reasonable but some obviously did not want to cede power for who knows why and the struggle ensued.
Awful job by SHU not to control this much earlier and not let it get to this point.