For example..if one civilization were to excessively drink alcohol and avoid excersize while eating only manufactured foods, and another were to do the opposite, could this over time, and over many generations cause a genetic mutation of one or both societies?
Probably not with this specific example, unless the diet/exercise was so extreme that it reduced fertility in a way that was not overcome by human technology. Natural selection would only weed out those gene variants that reduce survival prior to reproduction, or reproduction itself.
Though there are such possibilities as the "grandmother" effect; that is, older relatives who help ensure survival of their kin after they themselves have passed reproductive age.
Diet does influence mutation rate - processed/cured meats like sausage, hot dogs, and bacon are mutagenic; as are well done or seared meats. A diet high in such things may increase genetic variation, but would also increase incidences of diseases like cancer.
There is the example of a "high altitude gene" in Himalayan populations that allows better use of oxygen, and thus better survival of offspring, at higher altitude. Free full text of the article here:
Higher offspring survival among Tibetan women with high oxygen saturation genotypes residing at 4,000 m.
If you consider living at a high altitude as "choices that humans make today", than given the above reference, the answer is yes - the choices do influence the genetic code of their offspring.
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