As you conquer, you will end up with an army of workers. Have them trail your army and build a trading post for 1 turn over every farm, and a fort over the wheat. put Tp's on all the hills that don't provide food, they will starve down to something more managable.
Try to conquer up the happiness wonders as well. use nukes to capture cities that down have wonders, they wipe out population and pillage the country side. 2 or 3 dozen stealth bombers scattered arround the map will deal with rebels - just ignore hapiness. Once you have all the SP's you need just start annexing.
I usually don't make a total victory since its just more grind, but it would not be a problem to do so. I just ended a game where I started to steamroll with 9 SB's, ended with over 33 of them. I played the last 200 turns negative happy, and was in the negative teens or lower for over 50 of the last turns until I got the capitol of the games wonder whore. Once you reach a certain point, all that matters is gold. Loss of production and the very unhappy penalty in combat does not stop SB's from being overpowering...