Don't bother trying to go to Pacentro or Civita di Bagnoregio thinking you'll find real solitude: by now those places have become Instagrammable too, and especially Civita is always packed. Instead, aim for villages that have the same charm but stay peaceful because they're less well-known.
Montone is perfect for what you're looking for: it's one of those compact, well-preserved medieval villages where local people actually still live, not just for tourists. It has a nice central piazza, little uphill streets with countryside views, a few decent restaurants. In September it's still pleasant but without the summer crowds. Similar but even smaller is Lisciano Niccone, which sits on a hill and has that peaceful vibe you're after - it's exactly the kind of place where you arrive and the bar staff still talk to you naturally. If you want something wilder, Lupara is tiny and almost abandoned, kind of melancholic but evocative if you love bare medieval architecture.
Another option is Amelia, slightly bigger but still off the radar compared to the usual places. It has visible Etruscan walls, real history, and it's the kind of town where you can spend a couple of hours without feeling crowded. If you have time, Panicale is the compromise between "worth it" and "not too many people," as long as you go on weekdays.