Jon,
I am not an advocate of long-distance running for pitchers. I'm just saying it's worked for some, like Clemens. I agree with everything else you've said.
Rather, I am an advocate of cardio-conditioning for starting pitchers. Running, as you state, might be counter-productive to any great extent. But I think biking, walking, the stairmaster, light swimming, and even long-tossing can be an acceptable substitute. Without an adequate maximum oxygen uptake (MOU) the starter will eventually fatigue and adjust his mechanics negatively.