Hi Beth!
That sounds like a great trip and wonderful family activity!
There are not discounts for runners on marathon weekend because of the large number of participants. But, since it is in January and that is still Value Season at Disney World, the rooms are still a great price.
You definitely want to stay on property. Not only will that help everyone get around to the parks and other Disney properties, but all of the Disney resorts offer free bus transportation to ALL race weekend events.
Check out the
Value Resorts. These resorts are comparably priced to area hotels, but offer all of the magic and convenience of being on Disney property. And just like all Disney resorts, they are impeccably clean and have really fun themes. Once you've chosen a resort, you can call 407-WDW-IRUN to make your reservations.
Please let me know if I can help in any other way!