Its up to you whether to smoke or not on the diet but it does negatively effect the health of your gut and immune system. I recently quit during the week and only do this on the weekends now, and I feel a lot better because of this. Its all a personal decision.
One thing you will notice is that as you become healthy you won’t want to do unhealthy activities. This is what has happened to me and many others. One way I look at it is that smoking is great for when you are feeling bad, but its not always great when you are feeling really good. Why kick yourself down when you feel good, you know?