See, you asked for advice, and the only advice anyone can give is either "persuade her to stop" (which you say makes you feel guilty) or leave her, which you say feels silly. It's either one or the other, or learn to put up with it.
There is no benefit to smoking and if she's a smoker from 16, it does not make for a promising, healthy future. You should feel no guilt in trying to persuade someone you love to give up a pointless, almost self-destructive habit (provided you aren't relentless or preachy about it) that will ultimately lead to the both of you being happier and healthier. There's all manners of methods to help a smoker quit around.