Hi Rachael
You have my sympathy - I'm the same height as you, and very similar weight (ie. completely normal BMI), with a normal body fat percentage, and I get running-induced amenorrhoea at high mileage levels despite eating lots. I tend to shed weight rather scarily too, though hope I'm on top of it this time round.
But the doc in me has to say yes, missing periods is A Bad Thing for your bones in the long term. Nor, it appears, can the process be avoided by taking calcium supplements or oestrogens in the pill or HRT, and the weight-bearing exercise that we do doesn't protect us (although strength training, playing squash, and triple-jumping might because they make the tendons pull hard on their bony insertions and that stimulates new bone formation).
I find that reducing my mileage restores normal function very quickly, but that isn't much good if you're marathon-training.
It would be worth having a baseline bone density scan using DEXA rather than heel ultrasound (you may have to pay depending on the criteria used in your area for having the test on the NHS) and repeating the test annually if your periods don't return. One reading isn't terribly meaningful, but a series showing that you are maintaining your bone density would be reassuring, and a drop in bone density over a year would suggest that Something Should Be Done.
So I agree - back to the quack!
HTH, V-rap.