I think discussion about public order can be handled here better than in comment section.So let me explain few things:


Army presence within city walls causes disorder. Population of the city usually didn't like to have armed men within their walls for prolonged time considering single turn in GC represents 3 months.
And even if those troops were at home, still their presence within city would hardly improve what civilians think about their situation - they want protection from army, and that protection should be guaranteed by engaging enemies outside, not encamping in the city, eating their food and for enemy within walls - especially because sieges were typically nasty things, where attacker behaved harsher more resistance he met while attacking the city.. it was not that uncommon to loot and kill civilians and ventilating the anger of own losses during the attack.

From game perspective, this negative penalty is by no means high. when army is garrisoned in the city, it gives -8 to public order, yet this penalty can be quite often balanced out by general personal skills, so you might have certain Generals that will be able to actually improve orders even with army garrisoned in the city... (just don't expect it for every single general)

Now, if you want to improve order in the region, as General you need to secure that province. send patrols, yet have men ready to respond to any enemy potential movement. Because of this, Entrenchment stance now improves public order (+8),slightly increases defense stats of all army units, and more importantly, increases the reinforcement radius by 100%, therefore army in the camp can actually reinforce other armies or city garrisons in case enemy army passes through and starts sieging the city.

Another good way how to pacify the region are agents. Champion's ability to calm the population is definitely something you should use, but, you should not ignore the cultural background of the province.

Practically, golden rule is not occupying enemy province where your culture is not present to some degree. Which means if you want to punish some enemy, sack their cities, and leave them burning, but if your goal is to occupy the region, you should send dignitaries first, so they start converting the local population to your culture. Once you have good cultural foothold, then you can send the army and take the region, and you will not meet such resistance..

And of course, lets not forget the option to actually fight the rebels. With the R2TR focus on generals, having rebellions occur, is perfect way how to train your generals.. each battle you win decisively will grant you a lot of points to improve your general.. Each time you destroy the rebel army, military crackdown will reduce the provincial disorder (20 points!).. so fighting the rebellions presents some good opportunities (enslaving captives increases slave population, which in R2TR3 doesn't generate as much negative public order, but increases provincial income)