Also, if the civ isn't right next to you, the maintenance costs of taking over civ can make it not worthwhile in the earlier game. In the game I'm playing now, the Incas kept giving me **** for not being Buddhist and they had one city on my border and taking the rest would have stretched me too thin at that point in the game.
So I took that one city and sent my Jaguars running around the rest of their empire destroying stuff. They sued for peace and were so weakened another AI charged at them soon afterwards and they never bothered me again. Plus I got a ton of gold out of it, which let me keep running higher research while I was at it.