By the time the runners have gotten to the AK and Disney Studios, they are more spread out. So you won't have mobs of runners going through at the same time. They have 7 hours to complete the marathon and it starts at 6AM. You just need to keep out of the runners' way in these parks.
On Sat, after the 1/2 marathon (which runners have 3.5 hours to complete), they will have the Family Fun Run that begins about 9:30 or 10AM and goes through Epcot. This year, the 1/2 marathon goes from Epcot to the MK and back to Epcot, instead of finishing at the Pluto parking lot at the TTC.