Coming from a hippy family with a farm and yet going into the sciences has put me in an interesting position. I consider GMOs to be fine purely on their own merits (and fight with my family often about it) but the overuse of pesticides and herbicides and the resulting agricultural runoff you mention are a real problem, and not the only one. Much of the politics around GMOs and GMO labeling have been governed by the ongoing political and economic battles between large-scale industrial farms (who are very, very much not friends to the environment) and smaller, locally and family owned farms. Much of the opposition to labeling GMOs has come from large industrial farms- small locally owned farms are more likely to be GMO free and in favor of labeling, so the industrial farms oppose labeling for their bottom line.
So it's a super complicated issue that's being even more broadly complicated by the public's insistence on treating it as a ridiculous issue about the safety of genetic engineering. :(
Great post, though!