If it's mildew, it's progressive and you should treat it. If it's a stain (such as from rust) it has less effect on the cloth than would any efforts to remove it. I'm inclined to leave stains on, and just sail with an "experienced" sail. Sometimes the chemicals used to "fix" it are worse for the dacron (or kevlar, or whatever) than the original stain was.
As a kid, I regularly got beat by a boat with a "rhorschact blot" paint stain on the main which didn't seem to slow those guys down much.
If it's strictly aesthetics, I'd say leave it alone. If it's progressive moisture-based deterioration, then treat it.