I suspect the routes could be altered - they're probably working out some alternate solutions. As far as I know, both are still hoping for business-as-usual.

So far both the ATM and MCM are saying they will NOT be affected. Though I think that could change if the shutdown continues that long.

http://www.washingtonpost.com/blogs/early-lead/wp/2013/10/01/shutdown-wont-stop-marine-corps-marathon-army-ten-miler/

Will the ATM be affected by the shutdown? Isn't it mostly staffed by volunteers?