Traffic in DF is always a concern, and you have to factor in the cab ride from your hotel to the bus

1) I'll be in the DF 5 days. Thought I'd sleep in DF on 5th night then bus to Puebla early am Thurs , hoping to arrive by 9:30-10, but I hadn't factored in morning traffic. That's probably rush hour-so the 2 hour ride might be longer? What is AM traffic like DF to Puebla? - perhaps it's better to sleep that night in Puebla.
Traffic in DF is always a concern, and you have to factor in the cab ride from your hotel to the bus station as well. Generally, the bus company will factor in traffic concerns into their schedule, but caca pasa. Everything unsold last minute airline tickets in Mexico seems to take longer than you might think, so its best not to try and rush things. It is a vacation, after all. I can't speak specifically of Puebla markets, but most markets in Mexico are open before 10 unless its a market that caters more to tourists. As far as doing the market before you leave on Sat., it seems like a bit of a rush, but some of that depends on where your hotel is etc. If you don't get to do the market unsold last minute airline tickets in Puebla, you probably won't miss anything that you wouldn't see in Oaxaca. You can also buy your ticket to Oaxaca when you arrive in Puebla from DF with no problem.
As said before, traffic is always a problem. Just be patient. The churches by the zocolo are open before 10. Buy your bus ticket when you first get to Mexico. There are many places in DF to buy them. Ask your hotel for the closest. The things that are unique to Puebla are the candies and the pottery. Most of the other products you will find in Oaxaca.
A super-easy way to travel between DF, Puebla, and Oaxaca is Wayak Bus. Nothing wrong with going by the regular intercity buses, but this either picks you up, or you can go to a central location, and the price is comparable (at least when I did it). It's like a minivan ride rather than a coach ride.