The whistle-blower's perspective on it will always be a crucial consideration, if only to manage their expectations actively. In some situations, their consent to a particular strategy will be required, and legally required, I would think. In other situations, they wouldn't have the final say, in effect, but you would certainly want them to be agreeable to it.
The other thing is that in some situations, the best thing that can happen is for everybody to just confront the conflict that's in the workplace or in the organization. If it's a low-level conflict that can be confronted by management just telling everybody to, as we would say, “pull their head in”, and understand that the agency won't tolerate any lack of respect for the due process, then everybody may just get on with their lives. Simply with support-type protection, a whistle-blower may be able to just survive in that workplace, and that may be the healthiest thing.
It's very context dependent. There just needs to be a full suite of options available for managing the situation and the right people put in place to make those decisions in consultation with the whistle-blower, definitely.