There is a big discussion going on right now on how to find the balance between authenticity and artistic freedom in photography. I guess this all started with a move by a photographer combining a foreground with a sky from a different time an place, but the discussion has left this case and is now more fundamentally rooted. I thought a while about it and will try to make my (subjective) point.
First of all, I think that you have to distinguish between real and realistic. The one thing is what IS out there and the other thing is what COULD be out there. By taking a picture with a camera, we can only strive for it being a realistic representation of reality, for any reproduction by a camera is not real. This has important implications: I believe that there is no difference between an image that is straight out of camera and a post-processed image in terms of it being real, both are not real at all. By choosing white balance, composition, shutter speed and many more things you interprete the scene every time you click the shutter. So with every photo we create, we are on the continuum of realism and not reality! So stop saying that an image is not real, it never is.
Second thing is to evaluate, how realistic a nature photograph should be or how much manipulation it can cope. I believe that there is no definite line between realistic and not realistic and we should be as open minded as possible to everyone who defines his personal approach to this continuum. As Justin Reznick once put it, we are not taking a photograph, we are making photographs. This nails it because it consideres the creation of a photograph to be an artistic process, not a documentary one. So please let everybody decide for themselves where they draw the line in the processing.
I personally handle it this way: My photographs are subjective representations of real places, so I strive to bring a personal note to them but try to stay authentic to the place. That means I have no problems whatsoever with adressing color, white balance, exposure, shutter speed, contrast and so on on global level. Also I believe that blending exposures with different focal points or shutter values lend itself to this approach. Same goes for minor cloning jobs, e.g. for branches that spoil a small part of the scene. I draw a line when altering a scene goes that far that another human standing at the same spot would be irritaed not to be able to recognise certain elements. This means, I'm reluctant to alter big parts of the environment like combining foreground and background from different places.
So the big question is: What about sky replacement? I do not consider the sky a part of the actual scene, because it's not a permanent part of the environment. Clouds are epheremeral, they move from here to there. So infact, another sky could be realistic and I would not say that this a no-go in nature photography. I actually did it once where I photographed landscape and sky one day apart roughly in the same place and they went so well together and fitted my subjective view so well, that I went for it. But there is a but! Replacing skies is almos never easy, as is has a profound effect on the landscape light. So don't make it an easy habit as it might not be realistic at all. And second, I think it is counterproductive to artistic ethics and motivation to go the easy way and shoot whatever light you see and just replace the sky. It's a challenge, a motivation and a passion to experience the landscape and the light coming together and this is where the final image is linked to the personal experience. I consider the photos, where you can feel this link, this personal experience the strongest, the most valuable of all. So go hunt the light, chase the skies to the locations you admire!
Final note: The whole discussion about authenthicity and reality has implications to honesty. I encourage any nature photographer to be upright and honest about the post-processing. There is no point denying a sky replacement, as it will not make this image more real. Just be open about it and do not diminish those who did chase the light to the places.