My wife and I did the C&O full length years ago in November, the major downside of doing it later than October is the towpath is covered with leaves in many/most places and you can't see the bumps as well in advance. Many mornings we woke up to frost, but temps were usually in the high 40s and mid 50s by midday.
The other downside is shorter days - we did it in 3 60 mile days, and it wasn't really a problem. Doing it in two days with short daylight is probably not a good idea - even with 60 mile days we were limited on how much exploring we could do and still not ride in the dark.
The good news it is usually drier. Temperature-wise, with the warmer temperatures we now have, I'm still doing section rides in December most years!
A friend and I hiked 6 miles on the towpath around Harper's Ferry yesterday - while there is still a road closure, the towpath is in very good shape there at least.