He has not even been given a court date to argue his case. He has requested a hearing to reverse the decision to deny his aliyah but there has been no response.
Oh, and he put his life on the line in the IDF.
Yep, a non-citizen who commits a crime isn't granted citizenship, just like in the United States. Amona was an illegal outpost. There was violent resistance to it being removed. Your son knew what he was doing and will suffer the consequences of his actions.
Oh, and in the U.S. a non-citizen can get citizenship by serving in the military but it isn't automatic. A non-citizen who commits a crime in the U.S. would suffer pretty much the same consequences.