That was out of the bag pretty much as soon as Agnes got over her murdery phase. Also, it seems like she was already on Raffle's conspiracy radar.
No, I don't mean when the crew of La Sirena figured it out. I mean, when were they able to prove it to anyone that held rank in Starfleet? Why did Commodore Oh not just take command of a fleet of Starfleet vessels under some pretense?