Isn't raising taxes a global event though? It seems like no matter how much I minimize my unrest (which, as the OP noted, is very easy to do in most of your cities,) I always take a production and research hit when I raise taxes. While the production hit isn't the end of the world (slave pens, buyouts, spells, etc. can all mitigate the problem,) the research penalty doesn't really seem worth it in most cases.
Converting overflow pacification (i.e., negative unrest) into extra resources would be an elegant solution, because essentially it would be mimicking an increase to taxes on a city-by-city basis. Additional research technologies could allow the player to choose to use their negative unrest for research, production, or mana instead of gildar.