indeed, the diplomat, assasins, and spies are the greatest weapons at your disposal and the more you use them the better they become at doing their jobs.
assasinate the general/leader then spy on (cool note, spies will open doors for your invading army so you dont have to seige) also you can sabotage cities with assasins which is just too cool...
diplomat's are good for setting up trade and bribing a generals army.
as for rebellious cities, they are a true pain in the butt i've found... best thing i've found to counter it is to retake the city after then booted you out but choose "exterminate" population. then there is no more rebellious swine to worry about.