The inaugural-and-only Disneyland Marathon in 1995 finished in the middle of the day on Main Street; park guests were kept on the sidewalk, and the world didn't come to a screeching halt.
Similarly, the first couple years of the WDW Marathon and 5K ended in Epcot on the bridge between Future World and World Showcase, though I can't find a photo at the moment
Marathon Weekend was originally created as a way to fill hotel rooms during one of the quietest weekends of the year, immediately following the holiday rush. Since then, it has evolved into WDW's single most profitable special event of the year. Runners spend more than the average guest on race registration (mine was nearly $600 for Dopey this year), merchandise, park tickets, hotel rooms, and food (gotta fuel for all those miles!)
A similar strategy has been adopted for WDW's other race weekends, using them as a way to boost attendance in the offseason (for some ridiculous reason, DLR's races are all holiday weekends). In fact, the entire cheer/football/WWOS concept is loosely based on the success of Marathon Weekend. To put it bluntly, Disney wants the runners more than the typical guest during these times. Yes, I realize that's harsh, but it's all about following the money
Yes, it would be great if there were ways to move park guests around property seamlessly during the races, but it's just not practical given WDW's use of limited-access highways (though the new interchanges on Osceola Pkwy should help for certain events). If you really want flexibility in the early morning hours, stay at one of the monorail hotels; otherwise, expect to sit in traffic until they're able to clear things up around 8-9am for Half Marathons, or around 1pm for the Marathon. Or just go to a park that's easier to access, like the Studios or Epcot