The official crossing point with Russia in this area is at Koidula, immediately north of Pechory (Estonian: Petseri), but Setomaa is littered with abandoned control points, seemingly unguarded wooden fences and creepy dead ends with lonely plastic signs. One road, from Värska to Saatse, even crosses the zigzagging border into Russian territory for 2km; you’re not allowed to stop on this stretch.
Be aware that crossing the border at any unofficial point (even if you have a Russian visa) is illegal and could lead to your arrest. It was in this vicinity that an Estonian security officer was controversially arrested by Russian troops in late 2014 and sentenced to 15 years in prison for spying. Estonia maintains that he was kidnapped from the Estonian side of the border, while Russia insists he was arrested on the Russian side. In light of the current tensions, you shouldn't take any risks.