What seems to be missing thus far in the thread is the relation between the purpose of the photograph (or the purpose of its use or publication) and the techniques of alteration "allowed" or prohibited. If National Geographic is implying that what is seen in their pages is what people would see were they to go to those places, then they build credibility by guidelines of what is acceptable manipulation, either before or after pressing the shutter button.
Clearly, photographs used for evidence in the legal professions, or for documentation in photo journalism, have very little leeway for alteration of the scene or object, either before or after the shutter fires. But a wedding photographer has no problem in removing zits and wrinkles from the bride, and that is not considered "deceptive," or dishonest.
One of the questions that draws long and vehement responses has to do with "when is a photograph art." I maintain that if one approaches photography as a tool in producing art, the clone tool does what the painter does with the scene before him, and that is to remove from consideration aspects of what is there for the purpose of simplifying in order to focus the viewer on what is important to the painter, or photographer.
I am also sure that before photography existed, and a main function of painting was to record (and interpret) a scene, there was much more of a tie between what was in the scene and what was actually painted. As photography entered the scene it left painters freer to interpret what they saw in more personal ways, and eventually leading to impressionism, abstract expressionism,, op art, etc. And at each step along the way were the traditionalists arguing that that may be done with paint, but it is not painting, or even art.
Certainly photography has been through many styles, from the pictorialists to the "everything in sharp focus" period, to the abstract, etc. There was even a rebellion against the salon style of photography as artifice, leading to valuing the snapshot look over the superconcern with formalism, where every image had one point of interest, oddly enough at the same intersection of thirds, etc.
As somebody who has used film and the darkroom since my first Leica iif 50 years ago, and who now embraces the freedom and new technology to create from an image of a scene what it is I saw in my imagination when I looked at the scene, I don't distinguish between photo-illustration and photography. I simply see the camera as a tool for generating the material I further interpret.
Mozart was accused of setting out to destroy symphonic music when he first included the clarinet in his orchestra. The 12-tone composers were accused of destroying the entire heritage of western music, and Mondrian's geometric paintings were seen as anti-art, where as Joan Miro actually claimed to be doing "anti-painting."
At every step of the development of our arts, there were people who argued with logic or not about the validity of what was being done and whether it was "true" to the medium in which it was done. At the same time, there were and always will be, thankfully, those who don't see a contradiction, and don't see a need to make fine distinctions in the definitions of their methods or materials.
I don't know just what got into me right now, but I feel very strongly that if you capture something with a camera, it is a photograph. Is using the warp tool in Photoshop any different from wrapping a mylar tube around the lens?