Did you read the article? Specifically the story of the business that made <10k deposits because they had theft protection of max 10,000 ?
By the time you "make a case" you're already out lawyer fees and risk your business being closed. Please read the article (again). IRS does not need to show that you were trying to evade reporting requirements to seize the money. They don't even need to file a case!
A statistic like that doesn't make things any more just for the 600, but it serves as some sort of guide for how much a cash business should worry about it.
This demonstrates an imbalance between ability to determine truth, and ability for the powers that be to act. It is dependent purely on abstract pattern. Other commenters have pointed out that that model can be used to accurately represent the behavior of innocents.
I'd much rather see data on the effectiveness of this law. Does it actually track suspicious activity? Does it work, and is the value of that work enough to justify the grief it creates to the few you refer to that the law affects?
Does it sound like the law is being used unfairly? Yeah.
Does it sound like the law as written is easy to use unfairly? Maybe, probably yes.
Would I oppose changes to the law intended to make it harder to abuse? No.
Do I think it is a major practical concern for a typical small business or individual? No.
I don't think it is inconsistent or difficult to hold all those ideas at once.