In today's New England Journal of Medicine, Drs. Harald Schmidt, Kristin Voigt, and Ezekiel Emanuel (chief of the department of clinical bioethics at the National Institutes of Health) break down some of the rationale:

[A] more general argument is that employees must take personal responsibility for actions that impose financial or other burdens on employers or fellow employees. Accordingly, smokers should be responsible for the consequences of their smoking, such as higher costs for health insurance claims, higher rates of absenteeism, and lower productivity. These costs amount to an estimated additional $4,000 annually for each smoking employee.

Business is business, and $4,000 is $4,000. But as Emanuel et al. go on to say, those kinds of arguments are too simplistic, concluding, "Categorically refusing to hire smokers is unethical." Because smokers are more likely to be at a disadvantaged end of socioeconomic spectra, it puts undue burden on them, in addition to "preempt[ing] interventions that more effectively promote smoking cessation."

The discussion is nuanced and divisive. Drs. David Asch, Ralph Muller, and Kevin Volpp wrote an accompanying commentary in this same issue of the New England Journal that said these policies can be a rational part of imperfect efforts to save lives. They describe these hiring practices as part of a spectrum of Bloombergian deincentivization, the extreme end of which would be outlawing tobacco. In this case, if you don't quit, certain jobs will be unavailable to you. But, again, it's unfair from the perspective that nicotine is one of the most addictive known substances and you're effectively discriminating against people who have a harmful addiction, and are also happen more likely to be poor minorities. Sixty-five percent of Americans agree that this is unethical.

Both perspectives are thoughtful and available in full here and here.