Your friend could have fought that one and won. As a FAA inspector it is his responsibility to write up the violation. Once that happens and he submits it, it is out of his hands. I can assure that the inspector was not back there just because he enjoys riding around in single engine caravans. The company was under investigation to figure out why they had the midair, in his report I am sure that he concluded that he had the reason. The reality is that it wouldn't hold up in court unless the whole airplane full of passengers signed an avidafit saying he flew through the cloud. Of course if the pilot had declared an emergnecy then there is not one thing that the FAA could have done to him. Maybe the 90 days will give him some time to think about it.