Meri, having been a Liaison attached to the Order via an alliance with Japan, and a supernatural being (which group the Order apparently tends to view as little better than livestock), most likely only knows that the professor possesses something for controlling what she persists in calling "supernaturals."
She feels that such a device is abhorrent, yet has a conflicting belief that some supernaturals need to be controlled (raging, destructive beings like ogres, for example, or vampires who are not in disciplined control of themselves like she is, for example).
She might or might not know the Doctor's original role in the Order. I'd say not, though she was told that only those with a certain smell or other identifiers were qualified to be her superiors, and that the heads of the order or their immediate subordinates only were in that group. The remains of that smell or identifier is likely what is making her so suspicious of him.