Has the impact of a practitioner's theological framework on pastoral counseling methodology been studied? Do any existing pastoral counseling programs take into effect how the theological framework concerning the doctrine of free will affects the counselor's therapeutic approach? For instance, an institution that gravitates towards theological determinism (such as Calvinism) might be more likely to adopt an approach based on radical behaviorism such as CBA (e.g. ACT, which has an underlying worldview of functional contextualism; or functional analytic psychotherapy), while an institution that leans towards theological indeterminism/libertarianism (such as Pelagianism or Arminianism) might feel more comfortable with standard CBT approaches.

From my experience, most pastoral counseling programs seem to teach some form of CBT without considering how the underlying worldview of the therapeutic approach conflicts (or agrees) with the theological ideologies of the institution and thus might create unintended countertransference. Has anyone dealt with this in scholarly publications or studies? Do any institutions who teach pastoral counseling directly address this issue?
I'm not sure I would agree that Calvinism is deterministic. Calvinists believe that God is sovereign and man is responsible. Calvinists also believe that the Bible is sufficient for faith and practice. As a result, some Calvinists would tend towards a nouthetic approach, such as Jay Adams and the Tripp brothers advocate. 

Indeed, I would definitely say that Jay Adams and the Tripp brothers have thought deeply about how their theological framework and worldview affect counseling. Read Jay Adams's book Competent to Counsel and Instruments in the Redeemer's Hands, by Paul Tripp. 

As for institutions, you could look at Adams's group, the Institute for Nouthetic Studies at http://www.nouthetic.org/, or the Christian Counseling &amp; Educational Foundation at http://www.ccef.org/.