I am a runner also and I ran a marathon last December. About 3 weeks after I finished my last training run, my cycle sort of reappeared and it's been sporadic since then. I am not convinced that my training had any impact on my cycle, because I had been having problems for well over a year at that point. And believe me, I've got no shortage of body fat either!
Since I've had problems for so long, I've tried to find some information on how much activity (particularly running) is too much. I know my dr was concerned about me doing too much running and some articles I have read say no more than 10 miles/week if you are trying to conceive. I haven't been able to find any concrete answers though. Right now, my running is pretty sporadic for a variety of reasons, although I continue to work out 6 days/week.
Also, my old dr (I have since switched) was pretty adament about getting me on a cycle of Provera to induce a period if I went more than 6 weeks. She felt 1. that there were some increased risks to not having periods and 2. that eventually the Provera-induced period might be enough to jump start my cycle.
I guess I'd advise you to do some research and talk with your dr some more if you still have concerns.
Take care,
Amanda