This old statement doesn't appear to make any sense until you find out that in this context, "prove" means to test. In that regard, the sentence means "The exception tests the rule", which is true.

While Intelligent Design is being pushed by many warmed over creationists, some of the better ones are pointing out cases where existing evolutionary theory may be weak. They're pointing out exceptions that are testing the theory, and that's a good thing for science. The moment we stop questioning theory (any theory), we've relegated ourselves to dogma which is the antithesis of science.

For over a thousand years, the pronouncements of Aristotle were taken as dogma. Eventually, more scientific explainations by people like Newton were used to explain the universe as we knew it. Newton's theories and laws were a given for centuries until the late 19th century when more accurate measurements showed flaws. Over a period of years, the discrepancies became too prominent to ignore, opening the door for Einstein and others with theories that better explain the observations. To date, relativity has stood all the tests thrown at it, but I suspect that one day we'll find discrepancies with it as well. Such is the nature of science when done properly and we all benefit.