Katie, great decision. Small, non-touristy towns call out for car rental though. Do your research- driving is different, even small towns have ZTLs. You will drive a stick shift-of course- need lots of insurance, including theft, and pay triple for gas, but your car will be tiny and efficient. Trains don't go the hilltowns. No worries, driving is no problem in the countryside as long as you do your research! It's not like home, if you don't assume it is you will be fine.
Pienza, Montepulciano are gems, but ahem, hardly non-touristy. Get a map and pick some towns off the beaten path. The tower at Radicofani is very cool. Don't expect people to speak English. Aquapendente and Castello San Bernardengo were fun, completely non-touristy stops. They are so non-touristy I hesitate to recommend them incase people ask me "Why on earth would you want to go there?" But, I found the stops interesting and delightful even if it didn't have E-ticket tourist attractions. Buonconvento was good for a short walk-though-- definitely not the tourist stop though. Avoid Greve, it was disappointing, Panzano is a few km south and is the superior stop. Castellina is a great stop on the way to Siena. Lots of Etruscan tombs dot the countryside, explore some side roads and villages.
No disrespect to RS-- its my primary travel guide-- but small towns off the beaten track are just not his thing. Rick focuses on destinations best served by train, you will need to look elsewhere for good information about stops along the Chiantigiana and in Tuscany/Orvieto.