We'll be spending a few days in southern Tuscany, near Pienza. One of the days is a Sunday, which from what I've read, means a lot of shops will be closed. I am debating between 2 options for a Sunday:

1) Do Stu's one-day drive around Tuscany. This has limited dependency on shops and places being open. It looks like Sant'Antimo will be open too.
2) Spend a day in Siena or Pienza. Do these bigger touristy towns like theses shut down on Sundays also?

We are thinking we'll play by ear and decide based on weather, but I would love to get feedback on if one option is preferred over the other.

Thanks

You could definitely spend a wonderful day exploring Pienza, Montepulciano, Montalcino etc. add Sant'Antimo and depending on the dates, the garden of the famous Iris Origo's La Foce (in your area) and it would be a Sunday well spent.
http://www.lafoce.com/
I would also suggest the excellent Caffe Poliziano in Montepulciano for lunch. I am pretty sure it is open Sundays.

http://www.caffepoliziano.it/

Sunday is a big day for the Italian middle class to go out for a three hour lunch with the entire family, from grandma to babies.

This has two things that might affect your plans: crowds at lunch and many restaurants are not open on Sunday for dinner.

Obviously, you won't be able to visit churches during Mass.

I would go to Siena for the day, and see the Abbey at Oliveto Maggiore on your return---after 15:00.