Makes sense to me too because therapy dogs go into situations where immune systems may be compromised. They would know what you feed because the owner has to pass an interview, fill out lots of paperwork, take an exam about therapy dogs and your dog also has to pass a strict test.
Even healthy animals can shed pathogenic bacteria that can affect the human companion team member and others. Certain individuals are at increased risk of disease if they encounter various pathogens, particularly people that are immune-compromised, very young or elderly. This basically describes most of the individuals Delta Society Pet Partners visit: Patients in hospitals, senior centers, nursing facilities, hospice care, rehabilitation facilities, and schools involving young children, among others.
They are responsible for your pet and his or her interaction with other animals as well as a public that is vulnerable to many immune system disorders. I am sure that this was a difficult policy decision, but I certainly respect that they made it.
As to knowing what you feed, they can't know. But the ethics of hiding this from your team would certainly be something that should be considered by any member who wishes to participate in such service.