There is a fine line between the day after soreness and real pain.
After any good workout, you should be sore. That is the sign that your muscles have been worked to their limits and pushed just beyond. This kind of soreness should last around 2 days. Being sore shouldn't prevent you from exercising more. In fact, moving, stretching, and ridding yourself of lactic acid may in fact help.
But if you are in true pain, the kind where regular activity is painful and the pain is sharp or tearing rather than dull and generalized - then you might be more than sore. If that's the case, further activity might make it worse.
Take time to evaluate and be honest with yourself. Are you using regular aches and pains to get out of a workout? Or could you be really injured?
I'm stuck in the latter category, much to my dismay. The quad and knee injury from the marathon are not going away. I keep trying to run, but have to stop after one mile. This is where I need to take my own advice and assess. Even though it kills me, my leg needs time to heal. It will hamper my weight loss not to mention the training for Park City half marathon next month. But sometimes not exercising can be just as important to your health as exercising.
So in the meantime, it's lots of yoga, Pilates and arm work. Running will just have to wait.