The word was out. The higher ups had enough. They had enough. How many more screwups were they willing to tolerate? So they made an example of Professor Hamilton because he had so little to lose. He didn't have a family of his own, due to having been consumed by work his whole life so he was made a scapegoat while the members of the now defuncted Cadmus were being reassigned. They arrested him the day after Luthor was imprisoned at Styrkers.
After Cadmus got shutdown, a lot of heads were beginning to roll off as so the members began to leave an abandoning a sinking ship for the greener pastures. Waller was forced to take a desk job with the condition that she would never participate in any known or unknown military projects in near future due to multiple catastrophes that occurred under her watch. General Wade Elling was also being made to take a desk job or he would be forced to go to The Hague for unauthorized nuclear launch when Doomsday was released which was embarrassing for a man of his statue.
In the end despite the claims of doing it for the country Cadmus became everything they opposed, an enemy. They had the right intentions but somewhere along the line, they lost their sight of who they were and ended up being far worse than Justice League.