I am answering from the perspective of a professional counsellor.
There has been much discussion on psychotherapy and religion, on whether can religion and spirituality be incorporated into psychological treatement. There are many strong and valid opinions on both sides of the fence. As mentioned in your question, some of the main issues in involving religion and spirituality in psychotherapy are about ethics.
The biggest concern in incorporating religion and spirituality in psychotherapy is when there is a difference in religion or spirituality between the helping professional and the client. Even in cases where both the psychologist or counsellor and the client have the same professed religion, there might still be some major difference in values between the two. In such cases, whose religious viewpoint are to be followed? Even though the general logic is to follow the client's, in actual practice it is harder to distinguish than on theory.
Some of the risks in practice when incorporating religion and spirituality in psychotherapy are imposing of values, discrimination, ineffective communication, not sensitive enough, or being too focused on the religion and spirituality aspect (failure to look at the issue apart from the lens of religion and spirituality).
However, there are also some who see religion and spirituality as an important part of psychotherapy, and have proved to be effective in using it as a part of their treatment. There are also many people who have benefitted from such therapies.
In short, I would say that religion and spirituality is one of the tools that can be used in psychological therapy, and just like any other tools (breathing techniques, counselling, assessment etc.) they can be beneficial when properly utilised, or bring more harm than good if abused.
There could be quite a few ethical issues a mental health clinician might confront, but the one coming the quickest to the mind is that of trying to impose, influence or convert the client to the practitioner's faith/belief set. It is certainly appropriate to gauge the clients beliefs and how importantly they play in their life. This could be done in the initial session, but from this point there are a few ways in which a clinician should approach the issue without crossing an ethical boundary. First, a therapist can encourage a client to utilize the clients faith as a coping skill. This has been effectively used to treat everything from anxiety to substance abuse. Secondly, if the client is expressing distress from a belief or religious practice a clinician can inquire and offer possible guidance on this issue. However, if the religion/spirituality is not one the clinician is experienced with or feels they can not remain unbiased about then a referral to a source that can address this is recommended. One side note, a clinician needs to be careful in regards to religion/spirituality and certain disorders such as bi-polar and schizophrenia, where beliefs and practice can be more harmful than helpful when the client is suffering from these disorders.