Well, there is no such thing as permanent waste at all. If there were, then we would have no bacteria, because bacteria can live forever.
As far as waste goes, while it is true that some products of metabolism are directly harmful to DNA, those are a minority. Most waste products are harmful because they accumulate in high concentration in the body. It is not that they are inhertently toxic, it's just that any compound present in a very high concentration in organism is going to mess things up.
The link between calorie restriction and longevity is an intersting one, but is not explained yet. My personal opinion is that it does not have anything to do with the rate of metabolism and generation of waste, but is rather a regulatory mechanism, which ensures quick change of generations when times are good and long generations when food is scarce.