RTR, in its customary bid for realism, has introduced mechanisms that can render rebellion much less likely. In the case of Rome, there were, indeed, cases of slave rebellion and provincial rebellion, too, but never to the extent that they occur in vanilla R:TW.
So what are these mechanisms? Well, for one, RTR let's you build your faction's religious structures much more extensively and without having to destroy any edifices to local deities. It's certainly what the Romans used to do and alien gods were introduced from far-flung provinces into Roma herself.
RTR also lets you invest time and resources into assimilating alien cultures into your own. Indeed, you usually have to do this first, if you want to recruit local troops (RTR calls them auxiliaries), or your own faction's troops locally. This can be a lengthy procedure.
These techniques allow you to choose whether you want to rule with an iron fist or invest in winning over your conquered populations. We know what the relatively civilised Romans did and we know what certain barbarian factions did and RTR lets you choose your own way of doing things.