Man it's no wonder all you people are talentless and broke.

There is no objective reality and that's
Sucker Punch

You were "nursing" a two pack a day habit?

Smoking babies?
You have to realize those were different times. Babies smoked. It was common. I myself was nursing a two pack a day habit until I discovered Pixie Stix as a tot Wait, huh? Ohhhh.
Seriously though, you want some logic for it? Karen Allen's character was probably a wee bit nervous at that point, and smoking is something she might do to calm herself in a moment like that.

A journey into the realm of the obscure:
http://saturdayshowcase.blogspot.com/

I kind of see what you're all saying but it's not that convincing - either way.
It was widely known in the eighties, that smoking had negative effects on a pregnant mother's unborn child.
John Carpenter and Karen Allen were both long time '
puffing, wheezing-weasel's
' in eighty-four.
Maybe that has a lot to do with it?
This film is only a cartoon after all, as are all of Carpenters movies. So maybe it's silly to expect a high level of clarity.
Her smoking at the start of the picture, just a sign of depression and her miraculous pregnancy
a chance at hope and a new beginning. But I suppose Mr.Carpenter didn't see it like that.
She was still as 'fricking' miserable and hopeless as before : )

At the time the alien knew almost nothing about smoking and wouldn't think much about it. He tried smoking himself but didn't seem to get it in an earlier scene. You gotta keep in mind this guys kind of a blank slate.

Yes and even drinking a bit isnt dangerous at all.
And this is a modern research result.

So it must be
that the scene on the train, ( alien-baby-daddy-scene ) was 'added in' much later on?
BIB No it isn't. If you are old enough you would realise that while the dangers of smoking were well known by then, the stigma attached to women smoking during pregnancy wasn't anywhere near as rigorous as today.
Your reaction though is pretty common when looking at films from a different time and extrapolating current behaviour onto characters from over 30 yrs ago .
Si vis pacem, para bellum

Or is the "alien" baby so amazing that smoking won't bother it?
All Art is pretense.