Isn't this issue of photo manipulation just another aspect of the very broad issue, 'What is truth?'
We tend to categorise works into 'Fiction' and 'Non-fiction', often perhaps not realising that it's rarely an 'either/or' situation. Works of non-fiction tend to be simply less fictitious and more factual than works of fiction, but they still contain fictitious elements, just as many works of fiction contain some factual elements.
It's often said that history tends to be written by the victors. We're all biased to some degree. Even scientists who strive to be as objective as possible, can fall into the trap of 'selection bias', an example of which is the current controversy over Anthropogenic Global Warming. You wouldn't expect a climatologist delivering a lecture on the dangers of rising CO2 levels to ever mention any of the benefits of rising CO2 levels. To do so would be counter-productive to the message he's trying to get across, and he might get the sack from the Climate Research establishment he works for.
When photographers, or people in general with a camera, take a photo, they are expressing a personal bias through choice of subject, degree of cropping, choice of perspective, choice of DoF, shutter speed and so on.
When photographers later process such images for display or printing they will continue to 'improve' the appearance of the image, in accordance with their personal biases and preferences, using whatever tools are available.
It's quite natural and normal for a photographer to strive to produce the most pleasing result for himself, and/or others, if he has the time and the inclination.
The issue of the deliberate addition or subtraction of major elements in the image as shot, should be viewed in terms of the potential harmful consequences of such manipulation.
Clearly such manipulation of forensic shots could be very dangerous and lead to miscarriages of justice.
Likewise, the manipulation of journalistic shots, in terms of adding or subtracting major elements to the original scene, could have disastrous effects that might provoke riots and result in deaths.
On the other hand, if a journalist were to remove some distracting and irrelevant elements in his image, prior to publication, such as a tree branch jutting into the image from one edge, or some overhead power lines that spoiled the composition, that would be unlikely to have any serious consequences.
However, this raises the issue of whether or not a photo-journalist should be allowed the discretion of determining what is an inconsequential manipulation. Perhaps it's safer and wiser to have the general rule in photojournalism, 'No manipulation at all, in terms of adding or subtracting major elements within the field-of-view captured.'
As regards the example of replacing the sky in a landscape with a more interesting sky depicting a streak of lightning, I see no problem with this. Is there any place on earth where cloudy skies and lighting strikes never occur?
The fact that the sky and lightning in a particular photograph was shot on a different day at a different location is of little consequence as long as no confusion results. However, if a photographer were to visit the centre of the Sahara desert, take shot at a recognisable location, then replace a plain and rather boring sky with a dramatic, cloudy sky depicting a flash of lightning, certain meteorologists might get confused if it is the case that thunderstorms never occur in the centre of the Sahara Desert. I think that might then raise some ethical issues.