I am a smoker and my boyfriend has had a vasectomy so we decided that I could/should go off the pill. Its been 1 month and I started my period as I should have, but it has lasted almost 2 weeks now. I talked to my doctor and she suggested I take double pills for a few days to stop it, but wouldnt that be counter-productive if what is causing the prolonged bleeding is my bodys way of adjusting to no pill?

Taking the pill and smoking isn't safe to begin with. So, doubling up on pills sounds extremely dangerous even if only for a short time. I'd either wait it out (the bleeding will eventually stop), or find another doctor. That one sounds like a quack.