I'm not a doctor or an expert by any means, but my completely unqualified opinion is that it's fine to work out when your muscles are sore, so long as you aren't actually injured. My personal trainer doesn't think this is a problem and when I do experience occasional soreness, the additional workouts don't seem to interfere with my recovery. The soreness should go away after a few days (maybe a week at the most, if you haven't worked out in a really long time), however, even if you are continuing to work out. If it isn't going away, you might be overtraining or you might have injured something.
My Before and After Pics
"Decide what you want; decide what you're willing to exchange for it; establish your priorities, and go to work." --H.L. Hunt
"Life has hills. Set the treadmill at an incline."