You are correct that there is a physical basis for many disorders that are labeled as solely cognitive issues, however, there is some middle ground here. You shouldn't downplay the effect cognition can directly have on the overall health of an individual. The tie between placebos and their effect on our immune system is not something you should ignore. Placebos are a hell of a thing, and double blind studies are really difficult to accomplish, for this reason.

Their is some underlying physical link between the two, somewhere, absolutely, and the faster we find a direct link, the better, but what if, for instance, the effects of a medical treatment for depression involving inflammation pathways can be counteracted by a lack of therapeutic assistance to help cope with the cognitive effects of depression?

We don't know a lot more things than we thought we didn't know, especially since this whole gut bacteria thing started rearing it's head, but we sure do know what can help, for certain cases. Overhauling our definitions of delineating what is "physical" and what is "mental" is a very current issue, however, the line may be blurring more than it is shifting, and many professionals are looking more and more away from just simply "here is mechanism, here is treatment."

Also, psychotherapy has proven to be, by far (for now), the most effective treatment for PTSD. Setting fire to the DSM won't change that fact.

From here (in 2008, granted):

The largest number of studies on psychotherapy for PTSD indicates that cognitive-behavioral treatments, as well as Eye Movement Desensitization and Reprocessing (EMDR), are the most effective types.