1. Will there be less civilians later on, or any other way for the game to stop you from farming civilians?
2. What's the penalty of simply chilling, waiting for your research and tax to accumulate?
3. Are revolts ever anything else than having to redo the same mission?

It's been some time, so I might not be 100% accurate here, but if I remember rightly:

1) There are civilians in all missions as they are all countries of the world except for the final mission. I can't remember if the final mission has civilians or not.

2) You can wait for research, but then it'll take you a lot longer. Why? Well, when you are in mission the time is still passing so you get your tax and research done whilst you are in mission, and once you've finished the mission you then have a new territory too, which gives more earnings through tax. So all in all, why wait? Might as well just get those earnings in whilst you take over the world.

3) Revolts are just having to redo the mission.