It was also in the era before the news could be quite so comprehensively muddied by 24-hour news cycles, celebrity gossip, social media eruptions and all the other components of the onrushing tide of Modern Media Bullshit, an era when investigative journalism was not only still a thing, it had teeth.
To play devil's advocate though, the Protectorate/PRT (particularly the Protectorate) is a hell of a lot less insulated from problems than most other alphabet agencies like the FBI.
The PRT can probably keep sourcing faceless goons for their swat teams, or whatever they call them, regardless of scandals. But while baseline humans with good equipment can deal with a lot of parahumans, the rare ones that they can't deal with will eviscerate them.
So the PRT needs the Protectorate, as a 'don't make us call them' option if for nothing else. And the Protectorate is
hilariously vulnerable to bad PR.
Hero's aren't dime a dozen mooks, each parahuman is by definition a very scarce resource. You can't train a parahuman, you can't mass produce them. You can't even reliably
find them, certainly not in their civilian identity. Which means that unlike pretty much any other organization in government service, the Protectorate
needs potential members to
want to join. And the pool of applicants is always going to be
miniscule.
And almost all the parahumans are traumatized paranoids to some extent or another.
The FBI can afford for most of their potential recruits to hate or distrust them, because there will always be plenty of other potentials who don't care about whatever scandal they get hit with, or don't believe the evidence. The Protectorate can't afford for the tiny subculture of potential recruits to see credible evidence that they're an abusive workplace.
And the PRT can't afford for the Protectorate to stop being a strong backstop for when they run into a parahuman that can break/ignore/avoid con-foam or trivialize bullets.
Which, to bring it back to this story in particular, is the entire reason that Taylor is in the position she's in. Her superiors, however incompetently, are attempting to avoid what to them is a nightmare scenario. One of their own didn't just say a bad word in public, or get a little too expeditious with a suspect. One of their own committed a serious, direct, life threatening crime. Against a civilian.
That might not destroy the organization. But it getting out would certainly mean at least a few potential heroes and/or potential wards staying on the fence rather than signing up. And given how precarious the hero/villain balance is supposed to be? That's probably several local disasters, at least.
And then the commander on the scene made it so very, very much worse for them.