Once the AI is gone, any resistors will be automatically pacified by units in the town (one per unit), but they won't go away without ground troops in the town (air units, naval units, and artillery units do not pacify resistance). While the AI is still around, resistors have a chance to be pacified each, but you can only pacify one resistor per unit.
If you make a worker using a foreign citizen, it will be a slave and will cost no upkeep. However, if there are both native and foreign citizens in a town, you may not get a slave. I'm not sure if there is a way to tell which you will get.
I usually build either wealth or libraries in newly captured cities after they are starved down. While starving I build settlers or workers. If I need culture, I build libraries. If I expect the city to become productive, I build a library. Otherwise I will probably turn it into a science farm, and I'll build wealth. If it is early in the game, I might build catapults (as they don't benefit from barracks), but artillery cost too many shields. (Note that I usually play culture/fast science games, rather than for military victories, and this greatly affects what I build.)