Now, all the footage of excercise in zero gee that I have see is of a guy strapped into an excercise cycle, peddling away. I think it's easy to understand how this wouldn't be a full body workout. However, what you suggest, running in a big treadmill much larger than that of spacelab, might be some help, because even though you're pushing with your legs your whole body is being jostled around. Something like this, incidentally shown in 2001: A Space Odyssey, might help slow down this effect. The problem is you can't have your spacemen in the gym 24 hours a day, or they won't get any real work done.
There is already a good example of what I am talking about. Consider the differences between the Apollo command module and the LEM. The LEM had to be shrouded on the Saturn to boost it into earth orbit, otherwise it could never have made it into space. Once in space, however, it worked just fine for transport to the lunar surface & back, because it was operating in the vacuum of space. But it could have never returned to earth. On the other hand, if the command module has been designed to do it all -- including the lunar landing & return mission -- it would have had to be so large that the spacecraft would have been impossible to ever even get off the ground. That is close to the problem we have with the shuttle -- it is designed to not only get the passengers into space and return them, but also haul up stuff for them to work on while in space (and often bring it back) -- stuff that could just as well have already been up there and stay up there.
If a space transportation system as I have described existed, then you could have both the rotating space stations with their artifical gravity as Arthur C Clarke first invisioned, and also zero-g facilities like the present ISS. Astronauts could be ferried back & forth between the two, on a daily basis if necessary. We could get to the point where nobody needed to work in a zero-g environment for more than 8-12 hours out of every 24, or maybe even less often. With a little experimentation the optimal balance could be found that would allow people to stay and work in space for years with no harmful effect to their health.