I dealt with rebellions several ways:

1) whenever I captured a city I always exterminated the populace.
2) I tried to avoid building any highly advanced farming structures so the polulation never got too far out of control.
3) whenever I was conquering in one region I used large follow up armies of poor quality troops to garrison towns.
4) I bounced my capital around a lot - during the Italy campaign I moved my capital to Rome to ensure that the towns did not revolt.
5) I tried to focus on one area of operations at a time and to keep my captial near that area (I found that cities were more likely to rebel if I had not owned them for long periods of time).

I sometimes wonder if I should have played on to defeat the Casse, but then again I am enjoying v1.0 alot!!