Mindfulness and Naturopathy - Contradictory?!?

I have recently became aware of an interesting contradiction in what I do!
The Naturopathic part of what I do - Herbal Medicine, Nutrition, and GAPS, are all intending to reduce, and heal those things that make us feel really bad, difficult emotions and foggy, or disturbed mental states. I want to clarify we wont get rid of the normal range of human emotions and mind states we experience, but the 'pathological' feelings and mental states which are above and beyond the 'norm' human experience.  
There’s something implicit in you coming to see me, that we are trying to get rid of these difficult feelings like depression and anxiety.

And yet the Mindfulness practices I take you through are based on allowing difficult thoughts and feelings to be there, and to open up to them and acknowledge them rather than trying to get rid of them. Trying to get rid of difficult thoughts and feelings is not only exhausting and distracts us from living our lives fully, it seems to distort and intensify them! The technical term for this is Experiential Avoidance.

So in Naturopathy we are working intensely at getting rid of, and in Mindfulness therapy we are absolutely not trying to get rid of.

Sounds contradictory?!!?

So how does this all come together?  
While we are doing all we can to help alleviate dysfunctional mind states and feelings, we are also acknowledging and allowing you to be the person you are today, as you are, including everything, even those difficult things you would rather go away.  And we are increasing your resilience and skill to experience whatever comes up and strengthen your contact with the present moment. And learn how to balance the intense emotions with being able to relax and unwind more fully.

For example, often thoughts come up around "this wont work for me" "I will never get well" and you can feel hopelessness or despair.  We all have those pop up time to time as we are trying to improve our health.  Can we see and feel these thoughts and feelings and allow them to be there and still take action to move towards better health and well being?

There is something about allowing the difficult thoughts and feelings to really show themselves, and even deepening into them, that brings about its own transformation and healing.

I would love to hear from you, especially if we have done some of this work together, how this sits with you?