1st, if you think high quality manipulation is digital only, look at Jerry Uelsmann's work from the 60's and 70's, totally amazing stuff, and all done in the darkroom!
I too sometimes manipulate images, should it be called PHOTO-ART instead of photography? Where do you draw the line between? If I take a 35mm slide, and there's a pop can, some other trash, and a kodak box laying in the forground, and I walk out and pick it up before taking the photo, is it different (other than cleaning up litter!) than if I Photoshop it out? How about a film shot with a pola filter, or B&W with a red filter, heavily changing the sky and clouds. Is this also different from computer manipulation to get a similar result?
And I certainly, in the past (Darkroom) have put in clouds from a different negative, where a sky was just plain boring. I've also done this digitally, and to do it convincingly is not super easy.
It would be nice if there was an indelible way to imbed in the image, something that made it plain that it was manipulated, especially if the manipulation was more than contrast, color balance, and other basics.
This is a tough subject to deal with, as manipulation gets easier. How will this affect future historians, researching a subject?