The first Etruscan city I took gave me a -25 penalty for conquest that lasted one turn, and a -10 political instability penalty that reduced one point per turn. The second city was a -33 conquest penalty that lasted one turn, but nothing new happened to the instability penalty. The overall happiness came back pretty quickly once I enacted the "Bread and Games" edict on the province (it adds 4 food and 4 happiness per turn).