I would rather argue that we simply are not that good at certain things yet rather than arguing an inherent goodness on part of nature. breeding implies a natural process over time which tries to modify the offspring at the genetic level to have certain traits. Genetic manipulation uses advanced technology to implant specific genomes into a gene (the exact terminology might escape me but I think I made my point). I don't see why one being natural or artificial or why how technical it is would influence whether it is a form of genetic manipulation.
Now, being less horribly sarcastic the fact of the matter is that people won't do what they are supposed to. People could in theory easily google how to keep a better diet but an actual expectation for people to do this is borderline absurd. Even if we assume people would use the almighty google, it is not certain that the objective of health and fitness would be reached. There are many factors to consider here.... Heck, in a extreme case changing your diet with a particular goal can harm you without specific and technical knowledge of how your body is currently working. Working out is not as easy as merely doing pushups or going to the gym, you can easily end up horribly hurt without even doing anything stupid. Ultimately changing a lifestyle is absurdly hard and would require technical knowledge (either from nutritionists or guys who actually know about the body and can help you develop a routine with specific goals and time-frames to gain adequate physical fitness). It is also unquestionable that things like alcoholism, obesity and many other diseases depend heavily on genetic predispositions. It would be far better for everyone -and perhaps even cheaper- if those predispositions could be dealt with as early as possible and in time that would be a very realistic possibility.
its not like all things natural are all that fantastic in the first place. How many instincts, predispositions or reflexes do we have which are leftover from pre-historic times(I don't recall any specific examples at the time but I have read plenty about that)? Many of the very processes which go on with us are part of survival mechanisms which simply serve no purposes these days due to how society has changed...