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Nonetheless, most occasions of pain result from peripheral stimulation and I feel that the former message really detracts from the peripheral contributions to the experience.

Yes, the "cause" may be elsewhere, but I think what we're trying to get at here is that the experience of the pain is constructed in the head, and without mediation by the brain there would be no pain. I guess a good example of this would be referred pain - when pain is experienced in one area of the body but the actual "cause" is elsewhere. I don't think that considering how the brain constructs pain and addressing it at the level of the experience would necessarily preclude addressing the "causal" event, but I think you have a point that in pursuing treatment of the symptoms the original "cause" should not be pushed by the way-side.