It's not impossible, but it's certainly suboptimal. I fell off the wagon this summer, the result of a night of drinking and a bit of good old fashioned stupidity. We've all got a bit! This fall, I resumed aikido practice after a few years away (not smoking related!) and am currently doing both. Kicking the cigs is hard--it takes a special sort of mental discipline, in my experience. The trick isn't willpower, exactly; it's not thinking about it. Once you start thinking about a cigarette, you're done.
Anyway, the point is: Don't let smoking keep you away from aikido. Let aikido, hopefully, take you away from smoking.