We were in Disney this January 10-19. I would 100% recommend going to MK on the marathon day! I knew it would take a little extra time on the bus so I didn't plan a rope drop or super early reservations or FP and we arrived around 10 AM. The crowds were so light this day! I think a lot of local AP holders avoid the parks during the marathon because there are a lot of road blocks and detours, plus the marathon finish line is over by Epcot, so a lot of the runners seemed to tend to stay in that area and don't make it to MK until later in the day, if at all.
If you have single park day tickets, I would actually avoid EMH days at parks because they tend to be more crowded. If you have hoppers and are morning people, you could RD the EMH morning parks and then head to another park.
Also, prepare yourself for Christmas decorations everywhere until after marathon day!
