I think your approach with the sit and wait calmly for the runner to pass you is a good option. I do that with my puppy and cars. Cars freak her out.
Another option is to turn and go the other way, and repeat this every time she lunges at something but this isn't as practical as the "sit" option. I haven't personally used it because my dog will lunge in every direction when she freaks out. But I've seen the method used on dog training shows on TV.
They get a co-operative jogger to run down the path in the dog's direction and turn the dog away when she lunges, and then repeat over and over... but I guess, to make this work you'd have to get your dog off the path the jogger was using. Like on an oval or field.