You do realize that all of the derived benefits of evolution were conferred upon populations that had to endure the mass-testing of a change in their environment, right?
Don't get me wrong, I'm all for ecological biodiversity and the stability in confers, but evolution isn't finished and to think we're living in some sort of steady-state paradise is an inaccurate way to view ecology. Do we know the long term effects of genetic alterations? No. Should we ignore the power of genetic manipulationm and return to a Rousseau-like state of nature? I'd say no.
Interestingly enough, most of the tampering you mentioned in your post is icedentally environmental rather than deliberate. Mad Cow's deisease is thought to have developed from livestock being fed the nervous tissue of butched livestock. Antibiotics in pork and chicken arose out of a direct response to the demand of consumers to keep prices low. Lead (and other metals, especially mercury) poisoning of fish has arisen due to the increasing amount of pollution our culture creates.
So again, I do sympathize with your concern and share it to a great degree, but I think most of these problems have come about because the owners/operators of these production centers see science as a means to improving their profits and blissfully ignore the other, less (forgive the pun) appetizing implications a rigorous appraisal of their operations by a scientist might illuminate.
For example, anyone with a rudementry understanding of evolution and the reproductive cycle of bacteria would strongly recommend against keeping livestock healthy by overmedicating them with antibiotics. This might work in the short term, but the bacteria reproduce so fast that resistence to the antibiotics would be selected for at an incredibly fast rate, so now you're stuck with the same problem and one less tool to combat it. Deliberately ceasing to "mess" with food isn't a flag that will rally many, but intelligently going about attempting to solve problems instead of deferring or ignoring them might not either. Still, I think it's a strategy that makes more sense.