Perhaps, but here at the bottom, I have had to report abuse and neglect to superiors before. It's not quite as hypothetical as you suppose in my circumstance. I know I would do it, because I have done it in the past. Been called a backstabber, and all that. No-- when you have responsibilities for others, those responsibilities trump "doing favors".
That's just it, though: you have a supervisor to whom you can hand these things, and clear, specific ethical guidelines to which to hold frankly fungible workers. That's not to say they're worthless, only that the ethical calculus becomes a lot clearer when you can just slot in someone else in short order and continue on.
Now, me, I don't get a supervisor. I don't get to make it someone else's problem when one of my minions crosses a line, and in general there are fewer than a dozen people who can do what I need at the level I need. If I burn someone for violating the rules, things don't get cured, people die who would otherwise have lived, and plans on which many salaries depend get rewritten. The trajectories of lives I've never met change, usually for the worse. Responsibilities to others can militate against strict ethics, too. Plus which, operating at this level leaves its mark on the psyche. I know you've never been through grad school to experience this yourself and it sounds hard to believe, but nobody who earned a worthwhile doctorate gets out mentally healthy, and the pressure cooker only gets worse as you go farther along. By the time they're useful to us, they're not exactly sane anymore.
So, yes, responsibilities to others trump "doing favors", but beyond the level of employee handbooks and company policy and HR departments -- when people expect you to write those -- the decisions get way more complicated. Sometimes I want everyone to dot their is and cross their ts and use their inside voices. Sometimes I'm just happy nobody tried to blow up the moon today. Mostly I'm trying to balance the two in order to reach an optimal state where everyone's in a suitable work environment and we're getting on with making everything better for everyone. In that environment, it's really tempting to deal with the little things internally, where everyone understands and there's some flexibility -- and at some point everything looks little next to the magnitude of what you're doing.
I can barely imagine what it's like when the millions become billions and you're responsible for not just one thing but everything for hundreds of millions of people. That's not to say it can't be handled wrong, only that assuming universal corruption is about a useless as assuming universal idiocy when trying to understand what's going on.
This makes a very large supposition: The people are irreplaceable because of very specific skills, coupled with a very large caveat-- They perform at a high enough level that that performance rating itself is not replaceable.
In this administration, it is not a handful of missteps of otherwise highly capable people. It has been pretty clearly demonstrated that the entire cabinet (more or less), engages in conduct that goes outside of what is LEGAL, let alone what standard policies are, or why those policies were instituted (since you went there.)
This is on the level of "Yes, he holds the title of neurosurgeon, but he insists on doing icepick lobotomies, despite the fact that they are now pretty much illegal. He abuses his position as a setter of policy to override those rules for his own satisfaction, and ignores all the clinical evidence of how undesirable the procedure is, and how terrible its outcomes are."
EG, somebody that you REALLY, REALLY, REALLY need to replace, or at the very least, put underneath some very strong oversight.
"Who will you replace them WITH?" is a valid question-- In the case of Flynn, he most certainly performed his duties as part of a team; I would start there, and do an ethics review, personality and skills review, and then start testing out prospects from those teams. It might be possible to retain flynn (and thus keep his expertise), after demoting him to a more restrained capacity, but he would still need to serve out whatever sentence is appropriate for his criminal behavior.
I would liken this kind of situation (given your angle in bioscience), to be like-- "He is one of the 3 people in the world who can do this work." coupled with "But he has started running his lab like it was fucking Theranos."
When somebody else manages his labs, and assigns him annoying oversight to assure his work remains good-- he can still operate as one of those top 3 people. He just can't work without his wings clipped, QED. (because the work quality flags, because standards and practices are not sustained, and he used his position to re-write the standards and practices to what he felt was comfortable-- and ended up with contaminants everywhere, like Theranos's lab.)
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