The harm to institutional confidence looks like it may have already been done by those who could have addressed it and didn't, if what's been coming out today about these issues having been raised numerous times before and not addressed proves to be true. Internally, it will confirm to soldiers that those at the higher ranks are never held accountable and never held to the same standard as they are. At this point, if the allegations do prove legit, the opportunity to be credible may have come and gone.
Externally, maybe there is some way to salvage some credibility still available, i.e. how the investigation is handled, how they go about prosecuting, etc.... maybe the public will forget that this is only happening in the light of receiving bad press and not because of integrity, but the troops won't.