I have been at the park the last two years that the marathon has been going on. If you are staying on site and you take the disney transportation, you really will not be affected at all. I was never delayed getting to the park.
I would alway hit MGM on the day of the run (both years), and would totaly forget that it was the day untill I saw the cones in the parking lot going into the park. It was fun to stand there before the park opened and watch some of the runner/walker. They even had some of the characters out cheering on the runners. Got some great pics of Piglet, Jessie, Buzz and Woody.