Here is an interesting paper from the 2012 Academy of Management, on the use of research evidence in managing organizations. It is based on a large empirical study of 6 leading knowledge-intensive organizations in the health industry. We found a diverse range of knowledges and different types of evidence being used, which were not always able to "speak to each other":
Conference Paper Getting beyond the Tower of Babel? Disparate evidence based ...
The service to which I belong, the palliative care units, has as its mission the evidence based on clinical, research and training.
If the training can be measured evidence-based (and we're trying to do it), I think that the organization can be measured this way.
then, I believe that research can be used to evaluate both organization, training. can be evidence-based research, but can also be qualitative research (for examples: narrative), provided it is implemented with methodological rigor.
In my opinion, in such institutions, there should be used highly performant IT programs in order to support the management (as the administration) of the whole system !
What should be a different matter, is the management phylosophy (acknowledged vision, mission, and values).
Maybe you can find useful the concept of "organizational integrators" discussed by professor Bratianu Constantin !
Good luck with your further research projects !