I agree with most thing you wrote. Our modern method of farming have destroy the soil structure and lead to washing away of fertile top soil. Chemicals have threaten important insects like bees such that China's apple farmers have to hand pollinate their apples. There is no end to the disadvantages, but personally, I still believe that we can still practice commercial farming while eliminating most/all the disadvantages. For example, researches are saying that rather than using antibiotics for growth promotion and disease prevention, safer alternatives like probiotics, herbal extracts, acidifiers etc can be use. Talking about growing your own food, I don't think we can achieve that because I wonder how many people will like to do that. You may have passion for it but what about the neighbour who even hate the crow of a cock (we're not talking about the 'stink' of animal poop). The few that are into permaculture cannot even meet the huge food demand in their country. So I don't think factory farming/ large scale farming should be scrap because small holders can't just meet demand. A great deal of this arguement can be found here: Factory farming - A Blessing or A Curse?