safiya, if you have a medical condition which prevents you fasting, you don't have to (but you know that!) - but you could always make up the fast some other time, if you feel that stopping smoking will improve your health in the immediate future. There must be precedent for that, or for similar medical interventions.
Purists would say that you shouldn't even take tablets during the fast - but for some medication, it works better if it's digested along with some food.
Seems to me you have two choices, either defer starting champix or decide to make up the fast days, later on.