The New York Times has an interesting editorial about free-range pork, from James E. McWilliams, a history professor at Texas State University at San Marcos. He's reportedly the author of the forthcoming “Just Food: How Locavores Are Endangering the Future of Food and How We Can Truly Eat Responsibly.”
Agriculture is full of tradeoffs. A lot of people would like to think that what's "natural" is best in all ways, but it isn't the case. E.g. free-range pigs have more contact with pathogens. Likewise, sows that farrow outdoors wean fewer pigs, because piglets die from exposure.
Although an intensive farrowing until looks more sterile, it saves lives. That's analogous to a hospital, a greenhouse or a fish hatchery: they look bad and unnatural, but they prevent unnecessary mortality.