It's a half marathon, 13.3. miles (Disney only does one marathon (26.2 miles) and that's in January). They start it at 5am, and Disney usually has a 4-hour course limit. Even though that is from the last person to cross the start line, it should be done by 10 or 11 at the latest, and they close the course on a rolling basis - meaning as soon as the last runner passes , they start the clean-up.
Looking at the course map from last year, unless it changes a lot, most runners should be through the parks (DAK is the only one it looks like they had extensive time in - they start outside EPCOT and run around World Showcase, then there's a small leg into DHS) well before opening), and the ending is at WWOS. Even if there are still runners clearing DAK when it opens, there will be a lane for them - and at that point it would be fairly easy to cross at designated points.
Even with the roads that are closed while it is going on, the bus drivers know alternate ways to get to any of the parks (the marathon (26.2 miles, in January) hits all 4 parks, and the buses still manage to get to all of them.
The half weekends don't really have much of an effect on the parks at all in terms of the race.