I don't think they are in anyway comparable. I am talking about a matter of health, which I believe is a perfectly acceptable justification for offering some kind of choice for people. Racism has no logical basis. Offering separate accommodation does.
I'm not imposing any value judgement on who is 'better', smokers or non-smokers, which is the case with racism. If smokers were able to smoke in a pub, that doesn't affect their behaviour outside of it, or how they view non-smokers. I doubt there are many 'smoker driven' beatings and killings.
Hope this clarifies things for you.