As you have most likely discovered, there are unique challenges inherent in designing a program evaluation system for an agency.  Program evaluation must fit the needs of an agency, taking into consideration the clientele, programs, and staff available. 
If you were design a research study to answer the same research questions addressed in your program evaluation proposal without the constraints of having to use a particular agency, how would your research design be different?  For example, could you design a clinical trial to test effectiveness of treatments?  Would you be able to randomly assign participants to groups and run a true experiment?