It would've been pretty easy to see what sort of health impact cigarettes had if there had been much rigorous study at the time. The common pesticides used on farm goods, quite to the contrary, have been very rigorously evaluated by numerous bodies, especially the FDA. The rigor is likely largely a result of the public's learned suspicion of everything.

While it's good to anticipate that there are lots of things that can cause cancer, it's not a scientific approach to take to assume that all goods are guilty until proven innocent. Nor is the naturalistic fallacy scientific--you fall into it with your comment on things close to the natural food chain being more likely to be healthy, if I take you to be referencing goods that can cause long-term health problems like cancer.

While you're right that it doesn't have to be a binary choice, it actually essentially is. More or less all GM/pesticide-treated goods have literally no observed downside, and so while we will continue to monitor long-term population health performance to ensure that nothing is causing any issues, right now we find that it is only a choice between more or less starvation; higher or lower food prices; better or worse produce quality; and higher or lower rates of crop damage, which can lead to health issues in those who consume tainted crops.