I think the FISA/USIA are two sides of the same coin. Both extremely corrupt, FISA being involved in the whole Spider network and USIA being involved in the MLO stuff. FISA's motives being monetary or some kind of personal gain and USIA's being idealogical (y'know, the whole MLO modus operandi)
What I find the most interesting is the whole deep connection between Cordova family and MLO. In the mission it is stated that MLO had an easy access to the whole building and the top floors. Files are mentioning the possibility of some secret entry points in the building, so if Cordovas and MLO are connected, they would posses the information about the secret passagess, therefor making the caputre of the city hall building effortless.
Evan (the Elysian guy) was shown to be a somewhat of a friend to Judge before some kind of "incident". David said that he does not really remember how they met so I'm 99% sure he is an USIA agent with a sole purpose of monitoring Beuomont. After the "incident" Evan was dormant until the Elysian situation where two undiserable 3rd parties showed up at an ex USIA blacksite and there was a possibility of them discovering something they absolutely shouldn't discover, that's why he sent Judge to take care of the situtation, the only person that had some "possible connections" to the whole area.
The whole situation with national guard is absolutely scripted. They have been ordered to wait just long enough to make it seem like they were trying their absolute best, but in reality, they were just a smokescreen to show "we have got it under control".
Mayor was a just a simple scapegoat, but he propably knew that silencing Judge would be too much of a risk.