We had a family reunion during Marathon weekend a few years ago. As someone suggested, do not drive yourself on Sunday of the true Marathon. Take Disney transportation. We were going to Animal Kingdom with our son and his family to meet up with my brother-in-law and niece. Those two are almost locals so know the routes in and out of Disney World and were just visiting for the day. It took them quite a while to get into Animal Kingdom and I believe they went somewhere near Magic Kingdom since roads were closed or had runners at some point.
For us, we just boarded a bus and the driver knew which way to go and though it was a slower and longer trip, no hassles at all.
After our visit, we took the bus from Animal Kingdom to the Epcot resorts and had the same situations but arrived safely. We then walked along Crescent Lake to enter Epcot via the International Gateway and I was impressed with how Disney had cones up so us walkers didn't interfere with the runners but could still go about our day. Once inside Epcot, still more cones and we had to adhere to the Cast Members directing us but it was painless.
So, I wouldn't say avoid anything but pay attention to the Cast Member directions. This is a true Marathon so us non-runners can't interfere with the runners at all. Disney did a very nice job of "enforcing" that without making anyone feel weird about it.
Been to Disney over 60 times and wouldn't hesitate to go again during Marathon weekend.