In general, I tell my athletes to avoid stretching when they have strained a muscle, mainly because I don't think that they would be able to determine what an appropriate intensity would be for stretching the injured muscle. In my experience, depending on the severity of the strain, some gentle stretching starting a day after the initial injury will not hinder the healing process.
I believe that the gentle stretching in fact helps align the muscle fibers that have received the micro-tears from the strain. Unless an athlete has been taught to limit themself to a gentle stretch, than I would just have them avoid stretching all together.
As the previous poster said, RICE is always good after activity, but some lower end/less intense dynamic ROM drills will help as well. For example, I wouldn't want them doing hard leg swings, but walking atlas lunges or walking knee to chest drills would probably help.
I really feel that too much "rest" is going to hinder the healing. Again, this is all depending on the severity of the injury.
Another big thing to look at is the antagonist muscle to the one that has been injured. For example, if you strain your hamstring, look at the hip flexor and quads. If they have a poor ROM, then the athlete more than likely has an anterior pelvic tilt.
That would result in a weaker hamstring and place the hamstring in a constant lengthened position. Stretch the quads and hip flexors and work on strengthening the hamstrings to fix that problem.