You don't have anything to worry about. The crowds that weekend are nothing like spring break/summer/Christmas crowds. This is actually one of the slowest times of the year.
The marathons are broken up over two days this year (half marathon on Saturday, 1/7, and full marathon on Sunday, 1/8), so you will probably want to avoid trying to get to the MK early either of those two mornings. Traffic, including bus transportation, can be VERY slow from early morning till around 11:00 or so heading up World Drive, around the MK resorts, and the TTC parking lot. If you visit any of the parks those two mornings, you will see areas roped off and runners making their way through the parks, but this should not hinder your plans too much. The CMs coordinating the event ensure that this is run very efficiently with minimal effect on other guests.
After the races are over (around 10am on Saturday and noon-1pm on Sunday), you will notice very little at all that would even indicate there was a race that morning, other than some people wearing their prized finisher's medals around the parks.
I will be running in the marathon, so I guess I have a different perspective on the whole weekend, but if I was not running it and I had happened to plan my vacation through that weekend, I wouldn't sweat it. It's still a very slow time of year for the parks.
Hope this helps!
Steve