My thoughts are that if you are getting muscle soreness, the running is great for your overall fitness. I've been into fitness (weightlifting, cycling, running, and, at times, swimming for triathlons). Now, my primary fitness is cycling and weights. However, I've tried getting back into running a bit and found the same as you, Markster, that I was crazy sore afterward. However, I look at this as a need for me based on that soreness (cycling isn't hitting the legs in all areas). If you keep running, the soreness will go away eventually.
And, cycling is great aerobically, but doesn't build up the bones like a run will.
FYI, I'm the one who posted this thread. I'm going to keep running for the overall fitness, just wasn't sure if it would help me, overall, with cycling.