Caesar talked of capturing cities in his book. Basically if a city closed its gates and forced a seige, once he took the city, he let his troops plunder the city. If a city surrendered on approach or with some negotiation, he did not plunder the city. Basically he made an example of the first city that resisted, so that future cities would not resist. And it worked.
In game terms, if a city resisted and was stormed, the player should receive money from plundering the city. If the city surrenders, no plunder and possibly unhappy troops. Once a city is conquered and plundered, much more likely the next cities in a state or area, without a significant commanded force, will simply surrender rather than fight.
I also agree on the problems of 100% loyalty. I just don't think loyalty was 100 percent anywhere. And I imagine in many places outside of Italy, dominate loyalty in the countryside was to their non-roman selfs. While cities might have higher loyalty with roman families and adminstration and troops to their particular emperor. So a region in the dalmatia countryside might have perhaps a loyalty of 60 percent to dalmatia and 40% loyalty to Severus. While in the cities, it might be the opposite, 40% dalmatia and 60% Severus. And even possibility of some loyalty to opposing emperors.
In game terms, if you advance into enemy territory, you are almost completely blind except in your immediate location due to 100 percent enemy loyalty just about everywhere. No idea where enemy armies are located except through cavalry recce while the defender always knows the location of the attacker's army. Huge fog of war advantage to the defender due to loyalty which I find unlikely in a civil war.
I also think all of these civil war scenarios should have spies available. I know they are available in one scenario.