We're already doing a lot to counter these problems. Read up a bit on the poultry watershed problems in Arkansas for example.
No it won't. All that would do is put the smaller farms out of business and leave us with the large factory farms that are the problem. Free range, in theory anyway, disperses their excrement and doesn't create water quality issues.
One of the links in that article you posted (not the original source like most links I read from there) claimed that controlling ammonia would cost about "$8,000 per ton in the winter". That figure is approaching acceptable control technology standard costs.
The USEPA has been making progress in air quality issues. In 2002, they withdrew California's explicit exemption on factory farming. In 2001 they settled an agreement with Premium Standard Farms in Missouri, which forced them to install air pollution control tech, fund a $300,000 environmental project, and spend up to $25,000,000 funding pollution control technology research.
What we all need to realize is this will raise the price of protein and possibly make free range and small farms more competitive. The problem with the latter is it is much more impractical to control emissions from small businesses as it becomes extremely cost prohibitive.