There are occasional mentions of tobacco (and Pasqualate disapproval of its use) in the series. While it's probable that Federation standard nanites were able to deal with its deleterious effects, Langhorne, Bedard, and Pasquale had every reason and the capability to force all the colonists to go cold turkey and not bring the culture of Nicotina to Safehold, so why didn't they?
I can think of three in-universe reasons to unleash the demon tobacco upon Safehold, none of which seem all that compelling to me, but are at least plausible.
1. While the archangels could easily have kept tobacco from being used by the colonists as of the Day of Creation, they were unlikely to keep the command crew from using tobacco and they decided they wouldn't be able to keep it from spreading later to the colonists.
2. They brought Nicotina along in case they needed to use nicotine as a pesticide and they did. But in that case, I'd think there'd be proscriptions against any other use in the Writ.
3. They decided that human behavior would likely lead to the use of some tobacco-like substance and decided it was better for it to be tobacco with its known effects than something else with unknown effects that might well be worse.
Out-of-universe, the probable reason for Safehold to have tobacco is to provide a point of commonality with the humanity the reader knows.
