The parks are not crowded at all.
There is a half marathon on Sat (goes from Epcot to MK and back) morning. It starts very early and will be done probably shortly after the parks open.
The full marathon is Sun. It starts at 6:00 AM in Epcot, then goes to MK, AK, HS, and back through Epcot. The race will still be going on when the parks open, but it's not a problem. There is an area roped off for the runners to get through the parks while they're open. You shouldn't have any problems touring the parks, and if you see any of us runners, please cheer us on!
The only thing that is tricky is getting around in the mornings, esp if you're driving, as some of the roads will be closed. It's probably best to rely on WDW transportation to get to the parks.
DH & I ran the marathon last year and went to MK later in the day. We walked right on to everything at 3:00 in the afternoon. The next day, we went to MK, AK, and Epcot, doing the highlights in each park, again, with no waits. Have a great trip!
