With you all the way Phump. Increase your route gradually, but most importantly don't cycle at a speed where you are out of breath. You need to get your muscles into a regime of working for you.
Trust me, once you start riding for longer distances you'll pick up speed and stamina, but your main aim must be to stop smoking. That's the thing that's stopping you from blitzing your commute without a second thought. I did it the hard way, forcing myself to ride longer and longer distances, starting with a mile or two, then doubling that, then (and I can hardly believe I survived it) a 20 mile off road challenge on an old rigid MTB that nearly killed me.
Settling down into a 7 mile flattish commute after that was comparatively easy, but it took me another twelve months to give up the fags. By that time I had ridden some long distance off-road rides, and on some very steep hills. I learnt to suffer, and get to the top, taking as long as necessary to get my breath back. Once I took the plunge and gave up smoking, I was able to double the gains, so much so that I now treat steep hills as a bit of fun. My new commute is six miles uphill, and in the three months since I gave up smoking I have cut 12 minutes off my time.
Use the bike to get fit, be prepared to suffer a bit to get there, and then use the fact that you have got yourself fitter not as a reason to give up the fags, but as an incentive not to start them again.