Since you have had such a good connection with him for three years, I would try to salvage the professional relationship if possible. Express your concerns and ask him if he is able/willing to put aside religion and focus solely on his services. It's important that he is honest so that the same issues don't arise in the future. It is perfectly okay to seek out a new pdoc if he is unable to keep his religious beliefs out of his practice. You certainly deserve the treatment that will fit your needs best. You may find you are better served by a pdoc who relies solely on scientific and evidence-based practices. I truly don't believe psychiatry is the right field to discuss religion.