I'd definitely leave extra time. The runs mess up traffic patterns, quite badly.
That said, how much depends on where you're coming from and where you're going to. One thing I might consider is parking at DHS and taking the boat across, entering through the World Showcase - but others who have done this before might have better recommendations. If you are taking Disney transport, maybe just leave yourself an extra half hour.
(I've been in the area for RunDisney events twice - the first time I took Disney transport everywhere and the second I was a participant, so I'm not the best source for this! But yes, definitely extra time!)