I think the issue here is one's conception of intrinsic "rights". If they exist, they do not cease to exist or come into being thanks to socio-political change. If inalienable rights exist, they have always existed for everyone, despite the myriad justifications offered throughout history to deny them to certain populations. I don't think many will argue the US has a great record in allowing the exercise of these rights, but I will argue the ideal is sound, and worth fighting for.
On to the issue at hand: yes, the employer "owns" the job, and has a right to hire who they want. However, the employer does not "own" the employee at all hours of the day, as long as they hold employment. At home, the employee is a private citizen, and has the right to live the life of a private citizen, engaging in whatever legal activity they see fit. When we allow the employer to follow the employee home, I believe we're going down a very slippery slope. This is happening now, and in my opinion, is contrary to the ideal of personal freedom. (Again, rights cannot be legislated out of existence, only ignored or repressed).
Employers argue employees that smoke are statistically more likely to require expensive medical treatment. Therefore, they have the right to deny employment based upon the smoker's decision to keep smoking. I cannot see how this rationale stops with smokers. The next logical step is to deny employment to the obese and overweight. I will not attempt to guess where the road goes on from there. However, I do predict citizen's rights will continue to erode in the name of corporate interest.
Again, my argument is valid only if you accept my premise. If you don't acknowledge individual inalienable rights exist beyond the scope of legislation, the debate needs to be re-framed. I'm writing from the assumption most Americans, even those against the use of tobacco, accept this as a foundational ideal. If I'm right, it's not too late to change how the debate is framed, despite the efforts of some to name tobacco users "deviant".