I do think it should be possible to take sides in some civil wars though. In EU3 you could let pretenders take your capital and give in to get a new king, this never felt to me like truly choosing the side of the rebels but more like a gamey tactic. It would be great if you could choose the side of the rebels. Have diplomacy and the provinces that support you where you can raise more troops, hire mercs for the cause.
Rebels shouldn't be buffed but they need to be taken more seriously. England should be able to support a rebel group that's at war with France for example. Be it war subsidies, a guarantee that no one else swoops in to quickly take some land or a full alliance where they will join the fight.
Now you don't just play squash the rebel but also isolate the rebel. The changes of a successful rebellion isn't just a lot of revolt risk all over, to much to handle. But also your relations with your neighbours (if they hate you they would support the rebels quicker) and the interests of your rivals. Protestant neighbours would support protestant rebels etc.
The Spanish civil war in HoI3 is a good example of how it should work imo. Maybe with some region/religion/cb dynamic tag system like Normandian (religous) indepence fighters.