I currently am 116 pounds overweight. I have been working out since the beginning of the year. I tried running 5 months ago, and was discouraged that I couldn't. Since that time, I have strength trained, done a variety of cardio workouts, worked with the elliptical and the spin bike. So I decided to try running again. It's not easy, but it doesn't hurt like it once did. I'm by no means an expert on running, and not a doctor. I decided to do the Couch to 5K program by Cool Running, and so far I LOVE IT! It eases you into it. Small intervals, and increasing each week. I continue to stregth train even more, so that I do not hurt myself. I do not push too hard, or go to fast. I hope that it does not hurt me too bad in the future, because it feels great right now. I think it would be far worse for me to be unhealthy and severly obese for the rest of my life (as I'm only 32), than trying to run ... but everyone is different.
I too talked to my doctor before doing all of this. When I first began workouts, I had terrible knee pain - due to arthritis. I was told that it would most likely get better with the more weight I lost. So I stuck to my guns and my knees rarely hurt now.
Good luck with whatever you decide to do. Ease into it. The elliptical machines are a great way to start off!