The Conscience Enforcement Authority is not the only organization which holds power over conscience-like operatives. At least one other agency exists, employing Asmodeus and possibly Belphegor as agents. Asmodeus's employer has no currently known name, but Asmodeus has referred to it as the organization, and Seraphim as the other agency.
The objectives of the organization are not known, but it is safe to assume that they are different from the objectives of the CEA. As Asmodeus explains to Boo, operatives in his organization do not necessarily need to play the dual good conscience/bad conscience role that agents like Seraphim do on a daily basis.