As a smoker, I feel I should add my two cents. She chose to begin smoking, that's completely her choice and you don't really have any place to look down on her just because of that. If you like her it shouldn't matter. I can say with 99% certainty that she probably didn't tell you because of the HUGE stigma around smoking. I hide it sometimes as well because, even though it's none of their business, I know people will judge my personality based on the fact that I smoke. Without even knowing the reason why I started. Of course, being in a relationship makes it your business now. But it's not your place to decide that she should quit. That's up to her. You can talk with her about it to try and convince her to quit buts ultimately it's not your decision to make, and you need to respect that. You basically reacted the way that she was afraid of in the first place, hence why she kept it secret for so long. Being a smoker doesn't change who she is a person. If it's a deal breaker to you, then end it, because she probably feels bad about it already, and I don't think she wants to hear another person ( on top of the people who probably already do) scold her. Keeping it a secret is a whole different thing, talk with her about being more open in the relationship. If you make her feel like she's a bad person just because she smokes, or give her an ultimatum of any kind regarding quitting, in my opinion you don't deserve her. We know smoking is bad, we've heard it 100 times and don't want to hear it more. Set boundaries like where she smokes so that it doesn't affect you. But don't make this a bigger deal than it really is.

Best of luck