Well, there are bunch of other "cost of doing business" like bribing politicians or govt officials to get work done, expense on lobbying, paying fine rather than doing right thing by businesses and so on. I don't see people at large take this as just a cost of doing business and not something to be fixed by setting up and enforcing rules.
I would say there really isn't any fundamental difference. Any system requires a balance, and you never want that balance point at an extreme because that's where one type of cost is at a maximum. If you squeeze out all freeloaders, then your enforcement regime will eat >90% of the resources. If you remove all overhead, then the freeloaders will consume >90% of the resources. That's as true of academia as it is of law enforcement and government. Police and the judicial system need some amount of leeway to keep things sane. "Bribery" is a strong word that is used to label a vast range of activities, and no human system has ever been created that does not contain some amount of influence and persuasion. (And mostly, we just choose to call it bribery if someone else is doing it. It's defined by who more than by what.)
Slack is important. Slack is necessary for things to move at all.
(Which is not to say that the systems I'm looking at today have anywhere near the right amount of slack. Almost all lobbying should be explicitly illegal IMO. Campaign funding should be heavily regulated and enforced. Universities should be regulated so as to prevent the profit-driven hellscape they have become, at least as long as they're going to be directly or indirectly receiving tax money. Pharmaceutical companies, congresscritters, law enforcement, the prison industrial complex, ... it's a total mess. And it's not just about using the regulatory hammer, it's about underlying incentives. Everything has been captured and monetized. It's gotten so bad that I feel like it would be only fair if I were to be paid for my vote, since it feels like it's going to be converted vote -> influence -> money ever more efficiently anyway. That's not the system I want.)
You're comparing lazy researchers in universities with corruption in government. If you don't see the obvious differences in nature and consequence, I'm really not sure what to tell you.
But in case it needs to be said, yeah, we should probably maintain some reasonably-effective process for weeding out unproductive researchers. Again, we had one that wasn't too bad long before the bean-counters ruined research.
I largely agree with your complaint but I don't think the causation is quite that simple. "Bean counters" didn't show up to a highly competitive field and decide to redefine the competition. It used to be relatively easy to get a faculty position, and there used to be a relatively small number of people/papers to keep up with. As academic science grew, both in the complexity of open questions and the size of the aspiring faculty population, there was going to necessarily be some changes to academic output and its evaluation.
Unfortunately they've hyper-formalized in an utterly homogenous way. It's such a disaster that perhaps a nepotism free for all wouldn't be quite so bad. But I do think there's a deeper discussion here about how academic research can scale in a better way, both to accomplish larger/more expensive projects and to handle increased application pool sizes.