Ha, I can answer this one. I have the official Red Vs Blue Ultimate Fan Guide which goes into great detail about the stuff in RvB. Including stuff we don't know. They also talk about exactly what you're asking. This is all canon by the way so what's in the book actually happened in the RvB universe.
It's formed as a message from the Councillor to the Director and it basically has him saying that with the death of Captain Flowers aka Agent Florida, the Alpha aka Church is vulnerable. So because he needs protection and the fact that Tex didn't just steal Church, the Councilor thought it would be a good idea to basically sneakily reveal Alpha's location to her, so that she would go and protect him.
There, that's how. It does actually make sense and it's also a lot better to actually read the message from the Fan Guide itself.