I'd feel like that is a bit of a cop-out for this story, the whole point of the Citadel seems to be to create a chokepoint for the Reapers to overwhelm. They'll have all these species in one place at one time to be gone through with a fine-tooth comb. Not to mention it seems the Citadel Council for whatever reason felt like storing their most vital
secrets on the mainframe of the Citadel itself. If the GDI continued their research on anti-Scrin weaponry I imagine they did research to stop the Scrin
Mastermind and its ability to do
mind-control. It also helps that GDI has had experience with Nod using mind-control technology as well, so they should be able to detect Indoctrination.