For Star Wars Darkside we left our 12 and 9 year old in the room at Beach Club while we ran the half. They were fine, and our oldest is responsible enough to watch her little brother. They pretty much slept until after 7, ate breakfast in the room, and were fine playing on their electronics until we got back.
Obviously, depending on what corral you are in for the marathon and how fast you run will determine how long they would be alone for. For both WDW marathons I have run, I did not get back to the hotel until a little after noon, and that was starting in the middle of the pack.