Is it inherently flawed? Yes.

But I think you're actually asking if therapy just doesn't help some kinds of pain, and I agree that it is better with certain issues. I think therapy is better at helping clients navigate the world - get over a fear of driving, etc. I am not sure how good it is at healing a deep pain like you mention, though I think it can help you learn to function in a way that minimizes the pain - learning self-worth, etc.