I'm not sure where exactly the construction is happening. My impression from Heather & Jen is that it is on Floridian Way over by GF and Poly, so I had a thought that the course would be re-routed to run down Main Street twice. Go in from the side and make the turn up Main Street, through Tomorrowland and Fantasyland and through the castle, like usual. Then either going back down Main Street after going through the castle or going through the other lands as normal and back out to the hub and back down Main Street. Or I'm sure that there are backstage roads that go back to the front of the park and then could go back down World Drive until you can cut over (maybe Seven Seas Drive, depending on where the construction actually is) and go back to Bear Island and continue on.
Problems I see with that are course congestion and if they managed to go down Main Street twice, there's not really room for spectators too and I would cry more without spectators than I already do. And can they actually go back to World Drive if MK is later in the race like it's been for a few years and still get everything open and cleared for day guests?
But like I said, I am not 100% sure where the construction is, and this was more of a thought exercise while out on a long run to kill time. All I do know is that they need to have at least the marathon running through the castle or people will riot.