I think a valid comparison can be made between asking guests to remove their shoes and asking them not to smoke for three reasons.
1. In asking guests not to smoke or to remove their shoes, you are asking them to observe a boundary.
One is asking the guest to behave differently than they might in their own home.
2. While there are health issues involved in both, the overriding issue is the inconvenience caused by either guests smoking or wearing shoes in the host's home.
If a guest lights a cigarette at a dinner party, nobody is going to die of lung cancer as a result. Likewise, if a guest walks a bit of weed-killer into the carpet, it is unlikely that somebody is going to die (not that one should not be concerned about the health implications of weed-killing being walked into the carpet).
The real issue is the inconvenience caused. Smoking will bring into the house smells that are not appreciated by the host and may result in cigarette ash getting into the carpet or furniture. A non-smoking host will not appreciate this. Likewise, the host will be inconvenienced by guests keeping their shoes on. Carpets and floors may be soiled or damaged.
3. There is a possiblity that the guest's comfort may be impinged by either being asked not to smoke or to remove her shoes.
If guests cannot smoke indoors, they will either have to suffer the craving or go outside in the cold to smoke.
Removing shoes is rather less likely to cause discomfort, but some guests might still be embarassed at being asked to remove their shoes or may be unused to being shoeless in another home. This can of course, be minimized if they are informed of the policy in advance.
Guests might also be embarassed at being asked to follow a 'house rule.' They might feel like they are being treated like children.
However, it is most likely that guests will not be at all bothered and will respect that the host behaves a certain way, whether in not smoking or not wearing shoes in the house.
If it is reasonable to ask guests not to smoke, it is perfectly reasonable to ask guests to take off their shoes.