Mark,
Moderate physical exercise actually boosts immune function. The only time you have to worry about physical exercise decreasing your immune system is if you start to over train, it's actually called "Over Training Syndrome" where instead of building or maintaining muscle you are wearing it down due to overuse.
Here's an article that gives you an overview of it.
http://sportsmedicine.about.com/od/injuryprevention/a/Ex_Immunity.htmRest is a very important part of training, cycling exercises are a very effective way to keep your muscles from getting to the over training stage as well. In weight training for example it's recommended to change up the specific exercises you do in your routine to keep from over training. I cycle my routines quite often to keep from over training and also to promote greater strength gains, which goes hand in hand. Here is another great article by bodybuilding.com that's pretty good as well.
http://www.bodybuilding.com/fun/poor-recovery-result-of-overtraining.htmNormally bodybuilders and pro athletes are on the cutting edge of fitness and nutrition sciences and are good resources for information. With anything however you'll also want to keep your Dr and or nutritionist in the loop with what you are doing.
Now there are studies that show that increased muscle mass helps in survival rates in cancer as well so definitely don't stop exercising, just be educated about it and listen to your body to not overdo it.
Hope that helps
Eric