The first business mentioned in that article certainly did structure their transactions with the intent of avoiding reporting regulations, under the advice of their accountant:

Convenience-store distribution is a cash-intensive business, and Hirsch said his accountant advised him that he should keep the company's deposits below $10,000 because banks didn't like the paperwork involved with Currency Transaction Reports.

The article states But there was no evidence of criminal activity, not that there was no evidence of intent (as the section I quoted makes clear, the intent was obvious).

Please note that I'm not making statements in favor of the law in these comments, just characterizing the facts as I see them.

ETA: as I keep reading, the second business was also intentionally avoiding the reporting requirements (after a teller told them how). The third one does not directly state that they were trying to avoid the reporting requirements.