The caste system exists to perpetuate Karagond's power not Shayardene nationalism, and not the church of Xthonos. Shayardene nationalism and the Church of Xthonos can both exist without the caste system, Karagond can not. It is too dependent on the massive blood economy that supports it.
You're painting the former with an excessively broad brush IMHO, and in the latter case you appear to be assuming that the existing nobility are not just the heart of the nationalist movement, but also its only possible leaders. I don't see why either assumption must necessarily be true.
I can just hear the Kryptasts cheering you on.
Lenin and Mao both tried to engineer a society where everyone had the same amount of power. They both failed. There are always going to be nobles, ie. humans with a lot more power than other humans who will find a way to pass much of that power on to their children, even if you refuse to call them "nobles". You can execute all of the old nobles if your revolution is bloody enough, but that won't stop the creation of a new group of nobles, aka "nomenklatura" attached to the new power structure. As for getting rid of the monarchy, I'm fairly certain that the Hegemony is even less ready for democracy than Iraq and Afghanistan were in 2005...
Trying to prevent these things comes across as tilting at windmills to me. Maybe he won't be called "King" or "Thaumatarch", but unless some sort of theurge-spawned ecological disaster occurs to make the region uninhabitable, I'm fairly certain there will be another monarch within a handful of years of Karagond's defeat. Maybe it will be your MC (whether he admits it or not), or maybe it will be the emperor of Halassur, but most likely it will be some 2nd tier
KGB colonel Kryptast officer embeded in the very industry you hope to preserve. Let's call him Vladímiros Putinos for no particular reason. He will end the chaos and disorder, end the hunger, and in the anti-helot backlash that follows, he will bring back the harrowings. He will be publicly hailed for restoring order even as he has all serious threats to his rule assassinated.
Christianity doesn't prohibit slavery either, and yet the abolitionist movement was empowered by the Second Great Awakening where many (but not all) devout Christians concluded that slavery was implicitly incompatible with the teachings of Christ. http://www.pbs.org/thisfarbyfaith/journey_2/p_5.html
I get the feeling Halassur harrows fewer slaves than the Hegemony given that it seems to be less extravagant in its uses of blood (ie. no ward wall of its own), and instead of making plektoi and other theurgic monstrosities they seem to be concentrating on making weapons capable of killing them.
I expect that Karagond will keep the ward wall up for as long as it possibly can. It's not clear at this point if it will be Karagond or the ward wall that falls first. Nor is it clear how long it will take Hallasur to notice, mobilize, and decide to invade once the wall does fall. Regardless, it shouldn't take much to keep Hallasur on their side of the mountains, but then again I'm not planning to wreck the lives of the officer corps in charge of the border forces the way you are.