The prosecuting authorities are not going to charge somebody with a crime for making payments to an employee, where nobody disputes that the payments were made or that the employee performed work, merely because the owner of a business later claims that the payments to the employee weren't authorized.

Am I correct, that the accusation at issue is embezzlement? That means a taking of company funds for one's own benefit, even if laundered through a relative, not the payment of funds to somebody who an employer later contends was not authorized to be paid (even while admitting that the work at issue was performed).