I think it’s one of those “you know I know you know” situations.
The guild doesn’t care about the sisterhood knowing.
The visit to the Emperor might even be intentional to let them know 😉
Because right after the visit, the Reverend Mother is prepared to kill Paul.
So they take her to Caladan, no questions asked. It’s in their interest.
I think the secrecy is only not to loose face.