Granted that this isn't real life, but I checked a few articles on the web (search on "supervisor-subordinate dating"), and the consensus seems to be:
1. Supervisor-subordinate dating is the worst possible case of office romance (from the point of view of the organization), since it could lead to either charges of favoritism or charges of coercion.
2. Supervisors should immediately report any such relationship to HR, who will probably try to break the chain of reporting ASAP. (this is probably Griss's deception)
3. Public PDAs and discussions of the relationship with other workers should be discouraged, if they continue dating. (so they were doing the right thing here)
So, if they follow the common rules, Grissom won't be supervising Sara any more, and will probably be reprimanded by Ecklie and HR. But I don't think they can make him choose between his job and Sara. What would there be to stop them continuing the affair if he chose the job? The administrators will probably just try to fix up the appearances of propriety from a legalistic point of view.
Of course, this totally leaves out any of the special legal concerns that they would have about handling evidence, etc.
And I think the really interesting repercussions would still be personal emotional reactions from the team.