I'm no expert at photography, but I don't think there is a simple, pure alternative to manipulating photos.. Any photograph is an imperfect representation of what was there, and every photographer manipulates to some extent, by what's included and what's left out, by choice of lens or aperture, by lighting. Just the fact that you're turning a three-dimensional scene into a 2-d picture with limited color gamut, dynamic range and field of view means that you're manipulating reality by taking the picture.
So I think the question has to be, what are the viewers' expectations about what you're doing to the scene? In some cases, this is pretty clear. Photojournalism has strict rules (at least in theory) that permit only minimal post-processing of images; breaking those rules is wrong and can get you fired. Abstract photographic art may bear little resemblance to reality, and no one expects it to, so anything goes as far as manipulation is concerned. For landscape photography, I do whatever I feel like. If I take a shot of a nice scene and there is an inconvenient pedestrian or street light in the middle, I will not hesitate to remove it. That's because my goal is to make a picture that I like to look at, not to document anything, and I make no claims to be providing a faithful representation of what was there. For example, this was a decent looking scene
But I liked it better after I'd cleaned it up a little:
Portrait or candid photography is where it can get tricky. I have no qualms about removing a pimple or razor burn from someone's face. (Other than a slight ick factor from working on skin blemishes.) I think that's what people expect from such photography, and that's what portrait photographers and painters have been doing since before there was digital photography, or photography at all. On the other hand, the amount of manipulation that gets done now to lots of magazine photos strikes me as absurd. is a relatively tame example. Such manipulations not only misrepresent the individual being photographed, but create an impossible (and potentially harmful) view of what humans are supposed to look like.