Late game you get access to a few methods.
There are two spells. One (Devotion iirc) is an Enchantment and while active on a city it reduces Unrest by a flat -10%. The other is one of the late-game "boost" spells (Blessing?) which costs a /ton/ of mana but permanently lowers Unrest by 5% and can stack.
Later on you also gain access to Prisons (Level 4 upgrade, -1 Growth to this city, -10% Unrest in all cities) and the Ivory Throne (Level 5 upgrade, -30% Unrest in all cities). All of these make Unrest something which can be alleviated eventually.