Here's my prediction of what happens:
1) Ray resigns in a cloud of suspicion - there's no hard evidence to prove what he did (thanks to Brass) but at the same time he's lost the trust of everyone around him. (Kind of in the same way Elle Greenaway was written out of Criminal Minds)
2) The new guy comes in as an interim supervisor or consultant to clean-up the shit-storm Ray leaves in his wake. He's assigned to investigate the team (the way Doggett was assigned to investigate Mulder's disappearance, only to be end up assigned to the unit he was investigating)
3) Catherine probably comes to realize that further career advancement is going to be impossible and chooses to resign and start working in the casino empire, but she agrees to stay on until her replacement can be recruited and trained.
4) The new guy finds at least a bit of blame for everyone during his investigation, but nothing that would be a career-killers, just career-stallers. He concludes that none of the CSIs have done anything to warrant termination, but there's going to be some red marks on their records and that it will take a long time for the general public to forget about recent events.
5) Ecklie decides that maybe the graveyard shift has become a little bit too close knit and decides that an outsider's perspective is needed in order to restore their credibility and makes the new guy the permanent supervisor. The team views him as an interloper but he quickly wins them over with his quirky personality and fine investigative skills, and tries to steer them back to their roots as scientists first and law-enforcement personnel a distant second.
6) Brass sees the writing on the wall and begins to think about retirement, but decides to stay around a little while longer to make sure that then new guy doesn't have some sort of secret agenda.