I'm not sure why you think therapy is not a form of real treatment. Cognitive-behavioral therapy and dialectical behavioral therapy have been proven to be effective for treating numerous biologically based mental disorders. They are not even slightly based on Freudian models.
For many cases it is more effective than medication or boosts the efficacy of pharmacological intervention.
Therapy is an appropriate tool for treating biological conditions. Patients with OCD, whose brain structure is visibly altered because it is a biological condition, respond surprisingly well to CBT and Exposure-Response Prevention based therapy. It is the recommended first line of treatment for the disease [1].
As someone who suffered from OCD, along with depression and anxiety, therapy is a successful way to adapt and overcome diseases that are firmly rooted in biological origins. I experience a vastly improved quality of life than I did years ago. Of course this is an anecdote, but the research backs up the my claims of efficacy.
Given that these diseases affect a network of neurons, learning to adapt to structural, biological or learned abnormalities in the network is crucial.
A study on CBT[2] and depression came to an interesting conclusion:
The evidence shows that that CT [cognitive therapy] is as efficacious as ADM [anti-depressant medication], and that its effects are more enduring. Thus, even if CT and ADM work through the same mechanisms in the same temporal order to reduce depressive symptoms, any enduring effects of CT must be produced by mechanisms that are not mobilized in the same way by ADM. The model that is proposed in this article suggests that CT helps patients learn to recruit prefrontal regulatory brain mechanisms – a skill that these patients could continue to use long after treatment ends. Exploring the neural bases of these effects should enhance our understanding of the nature of depression and allow us to develop more powerful and targeted preventive interventions.
Therapy works and most of all it lasts. Medication may work, but when you stop taking it, you're back to square one.
The most important aspect of this is the acknowledgment that therapy works, through mechanisms not activated by medication. Understanding why therapy works can open the doors to understanding the disease and new modes of treatment.
[1] http://psychiatryonline.org/pb/assets/raw/sitewide/practice_...
[2] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748674/