A study released in the England Journal of Medicine today noted that although patients often disagree with medical recommendations for religious reasons, most physicians intuitively navigate the tension between patient preferences and medical judgment.

Abstract from NEJM:
Background: Patients at times disagree with medical recommendations for religious reasons. Despite a lively debate about how physicians should respond to patients’ religious concerns, little is known about how physicians actually respond. We explored the ways in which physicians interpret and respond to conflict between medical recommendations and patients’ religious commitments.
Methods: One-to-one, in-depth, semistructured interviews with 21 physicians from a range of religious affiliations, specialties, and practice settings. Interviews were transcribed, coded, and analyzed for emergent themes through an iterative process of textual analysis informed by the principle of constant comparison.
Results: Conflict introduced by religion is common and occurs in 3 types of settings: (1) those in which religious doctrines directly conflict with medical recommendations, (2) those that involve an area in which there is extensive controversy within the broader society, and (3) settings of relative medical uncertainty in which patients “choose faith over medicine.” In response to such conflict, physicians first seek to accommodate patients’ ideas by remaining open-minded and flexible in their approach. However, if they believe patients’ religiously informed decisions will cause them to suffer harm, physicians make efforts to persuade patients to follow medical recommendations.
Conclusions: When religiously related conflict arises, physicians appear to intuitively navigate a tension between respecting patients’ autonomy by remaining open-minded and flexible and seeking patients’ good by persuading them to follow medical recommendations. In such contexts, religion and medicine are intertwined, and moral counsel inheres in physicians’ medical recommendations.
From: Farr A. Curlin, MD; Chad J. Roach, BS; Rita Gorawara-Bhat, PhD; John D. Lantos, MD; Marshall H. Chin, MD, MPH, When Patients Choose Faith Over Medicine: Physician Perspectives on Religiously Related Conflict in the Medical Encounter, Arch Intern Med. 2005;165:88-91.
The question of how physicians should address patient religious perspectives and preferences has been addressed by others, including Harold Koenig, MD at Duke University. Essentially the ethical conflict is one between medical paternalism and patient autonomy (or freedom of choice in health care), which can be navigated in a respectful way by engaging in shared decision-making. A robust informed consent process, one that includes discussion of CAM options, may help.
Related to physician acceptance of patient religious perspectives is the question of integrating spirituality into the health care system. The law regulates both medicine, and healing at the borderland of medicine and religion. CAM therapies such as energy healing, that occupy this borderland, raise a number of issues, including analysis of how law regulates spiritual healing, and whether it regards these practices as “health care” and “medicine” or “religion.”
Beyond respect for patient preferences involving spirituality or religion is the question of how to draw on spirituality in medical practice without crossing the borderline into religion, intruding on patient beliefs, coercing or defrauding, or otherwise falling into shadow practices, while yet offering the highest consciousness that future medicine can possibly showcase.
Although it drew on a small sample, the NEJM article suggests that contemporary physicians are more tolerant of spiritual practices and beliefs by patients than perhaps presupposed, and therefore more successful at navigating gaps between science and religion.