You make too many assumptions and overlook other things that are plainly questionable.
Just because the food does not kill a person directly it doesn't mean it won't over time. It isn't necessarily toxins that will do it it might be some genetic strain that makes something in our bodies react badly over time.
As for antibiotics they are far from harmless. They kill a lot more normal body cells than they do disease cells. In fact too much antibiotic will kill you.

Have you heard of the killer potato? Probably not as it has been pretty effectively covered up.
A synopsis of the story is this. Scientists were trying to develop a better potato. During the process they were testing the potato on rodents. At one point a certain strain of potato killed every animal that ate it. Turns out the modifications had altered the potato so that it was toxic to life. I forget the story exactly I read the book about it 12 years ago and it happened in the early 1990's. The scientists who tried to publisize this result were fired and sued to shut them up. It worked.