What you describe is the reason zoning laws exist. Its not good that people have to resort to violence in order to protect their homes or their premises. For both the homeowner and the factory owner, a zoning law that settles the issue before the factory is built is the best option.
Just as a factory owner is aware of zoning laws, that factory owner will be aware of those risks as well. Then it's just a question of what's cheaper, paying for sound insulation and quieter machines, paying for lots of men with guns to stand around doing nothing, or paying to keep repairing broken equipment and burned stuff.
In either case, that factory owner will likely get severely underpriced by another factory that decides to build in a better "zone" and doesn't have to pay for those extra issues, so, as someone else said, this one likely wouldn't survive long in the market anyway.
So zoning laws save the cost of hiring a militia. Good point.