Only a part of them. Specifically the ones at the mines.
Of course it will. Zeon is the best chance to not being a shithole for rathpike and his main problem with the thiefs is probably that they add to the chaos. If we remove the source of the chaos there will probably be a conciliation between the two, with the maybe soon-to-be former thiefs being the future intelligence and espionage arm of rathpike.
Ahhh, Valos is such a goddamn mess beneath the surface...
If the magnats family is any indication purges will have to be made either way. That's the biggest problem with nobility: No matter how they started, two or three generations in most families become insufferable. I could imagine a combination of your suggested paths in order to get rid of the worst of them, probably through the doctor. If anything the ranger path will probably be a cornerstone to further the chimera experiments, maybe even tampering them to make them less... excessive? Elaborate maybe? But that would also require finding a way to stabilize the doctor and atleast partially mend her trauma, which would also help in salvaging some of the plutocrat families. Frankly, everything in Valos is/will probably be interconnected with each other: Helping one subfaction will open ways to help the others and so on, with the best outcome requiring to progress each route evenly. The Urchins will be difficult to deal with by themselves, since they're a combination of the corruption of both the nobles and the poor and we don't know yet how much worse the head of the Urchins made all of this. Their route might simply involve turning the Urchins from his influence. In the worst case we'll have to sic the town guards on them and work from there. The main point of Valos is to secure the fleet to be able to make landfall on the continent and supply the armies anyway. Unless the monsters build ships/use sea monsters as invasion transports, the firepower of the fleet itself will be irrelevant, which makes actually helping the families optional since most of the merchant fleet is in the hands of civilians, like the skipper that ferries you around.
Damn I think I lost my train of thought a few times in that last paragraph and forgot some ideas and theories I had, it's fucking late here anyway...