if you are training up for an indoc (which is safe to assume) stop running and rehab your knee. it might only need a couple of days, try it, couldnt hurt.
personally if i were u i would start off with alot of basic stretching followed by a brisk walk. add more stretches with longer walks as your body adapts to your new excercise program. take it slow and make it fun. excercise is supposed to be enjoyable.